biblioDMRP.bib.bak

@Article{BussoLopes2021,
  author          = {Busso-Lopes, Ariane Fidelis and Carnielli, Carolina Moretto and Winck, Flavia Vischi and Patroni, Fábio Malta de Sá and Oliveira, Ana Karina and Granato, Daniela Campos and E Costa, Rute Alves Pereira and Domingues, Romênia Ramos and Pauletti, Bianca Alves and Riaño-Pachón, Diego Mauricio and Aricetti, Juliana and Caldana, Camila and Graner, Edgard and Coletta, Ricardo Della and Dryden, Kelly and Fox, Jay William and Paes Leme, Adriana Franco},
  journal         = {Molecular & cellular proteomics : MCP},
  title           = {A Reductionist Approach Using Primary and Metastatic Cell-Derived Extracellular Vesicles Reveals Hub Proteins Associated with Oral Cancer Prognosis.},
  year            = {2021},
  issn            = {1535-9484},
  month           = jun,
  pages           = {100118},
  volume          = {20},
  abstract        = {Oral squamous cell carcinoma (OSCC) has high mortality rates that are largely associated with lymph node metastasis. However, the molecular mechanisms that drive OSCC metastasis are unknown. Extracellular vesicles (EVs) are membrane-bound particles that play a role in intercellular communication and impact cancer development and progression. Thus, profiling EVs would be of great significance to decipher their role in OSCC metastasis. For that purpose, we used a reductionist approach to map the proteomic, miRNA, metabolomic, and lipidomic profiles of EVs derived from human primary tumor (SCC-9) cells and matched lymph node metastatic (LN1) cells. Distinct omics profiles were associated with the metastatic phenotype, including 670 proteins, 217 miRNAs, 26 metabolites, and 63 lipids differentially abundant between LN1 cell- and SCC-9 cell-derived EVs. A multi-omics integration identified 11 'hub proteins' significantly decreased at the metastatic site compared with primary tumor-derived EVs. We confirmed the validity of these findings with analysis of data from multiple public databases and found that low abundance of seven 'hub proteins' in EVs from metastatic lymph nodes (ALDH7A1, CAD, CANT1, GOT1, MTHFD1, PYGB, and SARS) is correlated with reduced survival and tumor aggressiveness in patients with cancer. In summary, this multi-omics approach identified proteins transported by EVs that are associated with metastasis and which may potentially serve as prognostic markers in OSCC.},
  citation-subset = {IM},
  country         = {United States},
  doi             = {10.1016/j.mcpro.2021.100118},
  issn-linking    = {1535-9476},
  keywords        = {extracellular vesicles; integrative analysis; lymph node metastasis; mass spectrometry; mouth neoplasms; multi-omics; oral squamous cell carcinoma; prognosis; proteomics},
  nlm-id          = {101125647},
  owner           = {NLM},
  pii             = {S1535-9476(21)00090-6},
  pmc             = {PMC8350068},
  pmid            = {34186243},
  pubmodel        = {Print-Electronic},
  pubstate        = {aheadofprint},
  revised         = {2021-10-30},
}

@Article{Fanelli2021,
  author       = {Fanelli, Amanda and Rancour, David M. and Sullivan, Michael and Karlen, Steven D. and Ralph, John and Riaño-Pachón, Diego Mauricio and Vicentini, Renato and Silva, Tatiane da Franca and Ferraz, André and Hatfield, Ronald D. and Romanel, Elisson},
  journal      = {Frontiers in plant science},
  title        = {Overexpression of a Sugarcane BAHD Acyltransferase Alters Hydroxycinnamate Content in Maize Cell Wall.},
  year         = {2021},
  issn         = {1664-462X},
  pages        = {626168},
  volume       = {12},
  abstract     = {The purification of hydroxycinnamic acids [ -coumaric acid ( CA) and ferulic acid (FA)] from grass cell walls requires high-cost processes. Feedstocks with increased levels of one hydroxycinnamate in preference to the other are therefore highly desirable. We identified and conducted expression analysis for nine BAHD acyltransferase   genes from sugarcane. The high conservation of AT10 proteins, together with their similar gene expression patterns, supported a similar role in distinct grasses. Overexpression of   in maize resulted in up to 75% increase in total  CA content. Mild hydrolysis and derivatization followed by reductive cleavage (DFRC) analysis showed that  CA increase was restricted to the hemicellulosic portion of the cell wall. Furthermore, total FA content was reduced up to 88%, resulting in a 10-fold increase in the  CA/FA ratio. Thus, we functionally characterized a sugarcane gene involved in  CA content on hemicelluloses and generated a C4 plant that is promising for valorizing  CA production in biorefineries.},
  country      = {Switzerland},
  doi          = {10.3389/fpls.2021.626168},
  issn-linking = {1664-462X},
  keywords     = {BAHD acyltransferases; biomass engineering; biorefineries; ferulic acid (FA); p-coumaric acid (pCA)},
  nlm-id       = {101568200},
  owner        = {NLM},
  pmc          = {PMC8117936},
  pmid         = {33995431},
  pubmodel     = {Electronic-eCollection},
  pubstate     = {epublish},
  revised      = {2021-05-18},
}

@Article{Silva2021,
  author       = {da Silva, Viviane Cristina Heinzen and Martins, Marina C. M. and Calderan-Rodrigues, Maria Juliana and Artins, Anthony and Monte Bello, Carolina Cassano and Gupta, Saurabh and Sobreira, Tiago J. P. and Riaño-Pachón, Diego Mauricio and Mafra, Valéria and Caldana, Camila},
  journal      = {Frontiers in plant science},
  title        = {Shedding light on the dynamic role of the “Target of Rapamycin” kinase in the fast-growing C4 species Setaria viridis, a suitable model for biomass crops},
  year         = {2021},
  issn         = {1664-462X},
  pages        = {637508},
  volume       = {12},
  abstract     = {The Target of Rapamycin (TOR) kinase pathway integrates energy and nutrient availability into metabolism promoting growth in eukaryotes. The overall higher efficiency on nutrient use translated into faster growth rates in C  grass plants led to the investigation of differential transcriptional and metabolic responses to short-term chemical TOR complex (TORC) suppression in the model  . In addition to previously described responses to TORC inhibition (i.e., general growth arrest, translational repression, and primary metabolism reprogramming) in   (C ), the magnitude of changes was smaller in  , particularly regarding nutrient use efficiency and C allocation and partitioning that promote biosynthetic growth. Besides photosynthetic differences,   and   present several specificities that classify them into distinct lineages, which also contribute to the observed alterations mediated by TOR. Indeed, cell wall metabolism seems to be distinctly regulated according to each cell wall type, as synthesis of non-pectic polysaccharides were affected in  , whilst assembly and structure in   Our results indicate that the metabolic network needed to achieve faster growth seems to be less stringently controlled by TORC in  .},
  country      = {Switzerland},
  doi          = {10.3389/fpls.2021.637508},
  issn-linking = {1664-462X},
  keywords     = {C4 model; biomass; energy sensing; metabolism; nutrient sensing; plant growth and development; signaling; target of rapamycin pathway},
  nlm-id       = {101568200},
  owner        = {NLM},
  pmc          = {PMC8078139},
  pmid         = {33927734},
  pubmodel     = {Electronic-eCollection},
  pubstate     = {epublish},
  revised      = {2021-05-02},
}

@Article{Almeida2021,
  author          = {de Almeida, Jaqueline Raquel and Riaño Pachón, Diego Mauricio and Franceschini, Livia Maria and Dos Santos, Isaneli Batista and Ferrarezi, Jessica Aparecida and de Andrade, Pedro Avelino Maia and Monteiro-Vitorello, Claudia Barros and Labate, Carlos Alberto and Quecine, Maria Carolina},
  journal         = {PloS one},
  title           = {Revealing the high variability on nonconserved core and mobile elements of Austropuccinia psidii and other rust mitochondrial genomes.},
  year            = {2021},
  issn            = {1932-6203},
  pages           = {e0248054},
  volume          = {16},
  abstract        = {Mitochondrial genomes are highly conserved in many fungal groups, and they can help characterize the phylogenetic relationships and evolutionary biology of plant pathogenic fungi. Rust fungi are among the most devastating diseases for economically important crops around the world. Here, we report the complete sequence and annotation of the mitochondrial genome of Austropuccinia psidii (syn. Puccinia psidii), the causal agent of myrtle rust. We performed a phylogenomic analysis including the complete mitochondrial sequences from other rust fungi. The genome composed of 93.299 bp has 73 predicted genes, 33 of which encoded nonconserved proteins (ncORFs), representing almost 45% of all predicted genes. A. psidii mtDNA is one of the largest rust mtDNA sequenced to date, most likely due to the abundance of ncORFs. Among them, 33% were within intronic regions of diverse intron groups. Mobile genetic elements invading intron sequences may have played significant roles in size but not shaping of the rust mitochondrial genome structure. The mtDNAs from rust fungi are highly syntenic. Phylogenetic inferences with 14 concatenated mitochondrial proteins encoded by the core genes placed A. psidii according to phylogenetic analysis based on 18S rDNA. Interestingly, cox1, the gene with the greatest number of introns, provided phylogenies not congruent with the core set. For the first time, we identified the proteins encoded by three A. psidii ncORFs using proteomics analyses. Also, the orf208 encoded a transmembrane protein repressed during in vitro morphogenesis. To the best of our knowledge, we presented the first report of a complete mtDNA sequence of a member of the family Sphaerophragmiacea.},
  chemicals       = {DNA, Mitochondrial, RNA, Ribosomal, 18S},
  citation-subset = {IM},
  completed       = {2021-10-13},
  country         = {United States},
  doi             = {10.1371/journal.pone.0248054},
  issn-linking    = {1932-6203},
  issue           = {3},
  keywords        = {Basidiomycota, genetics; DNA, Mitochondrial, genetics; Genes, Fungal, genetics; Genome, genetics; Interspersed Repetitive Sequences, genetics; Introns, genetics; Phylogeny; Proteomics; RNA, Ribosomal, 18S, genetics; Real-Time Polymerase Chain Reaction; Sequence Analysis, DNA},
  nlm-id          = {101285081},
  owner           = {NLM},
  pii             = {PONE-D-20-26480},
  pmc             = {PMC7951889},
  pmid            = {33705433},
  pubmodel        = {Electronic-eCollection},
  pubstate        = {epublish},
  revised         = {2021-10-13},
}

@Article{Arias2021,
  author       = {Arias, Tatiana and Riaño-Pachón, Diego Mauricio and Di Stilio, Verónica S.},
  journal      = {Applications in plant sciences},
  title        = {Genomic and transcriptomic resources for candidate gene discovery in the Ranunculids.},
  year         = {2021},
  issn         = {2168-0450},
  month        = jan,
  pages        = {e11407},
  volume       = {9},
  abstract     = {Multiple transitions from insect to wind pollination are associated with polyploidy and unisexual flowers in   (Ranunculaceae), yet the underlying genetics remains unknown. We generated a draft genome of  , a representative of a clade with ancestral floral traits (diploid, hermaphrodite, and insect pollinated) and a model for functional studies. Floral transcriptomes of   and of wind-pollinated, andromonoecious   are presented as a resource to facilitate candidate gene discovery in flowers with different sexual and pollination systems. A draft genome of   and two floral transcriptomes of   and   were obtained from HiSeq 2000 Illumina sequencing and de novo assembly. The   de novo draft genome assembly consisted of 44,860 contigs (N50 = 12,761 bp, 243 Mbp total length) and contained 84.5% conserved embryophyte single-copy genes. Floral transcriptomes contained representatives of most eukaryotic core genes, and most of their genes formed orthogroups. To validate the utility of these resources, potential candidate genes were identified for the different floral morphologies using stepwise data set comparisons. Single-copy gene analysis and simple sequence repeat markers were also generated as a resource for population-level and phylogenetic studies.},
  country      = {United States},
  doi          = {10.1002/aps3.11407},
  issn-linking = {2168-0450},
  issue        = {1},
  keywords     = {Ranunculaceae; Thalictrum hernandezii; Thalictrum thalictroides; draft genome; floral transcriptome; pollination syndrome; sexual system},
  nlm-id       = {101590473},
  owner        = {NLM},
  pii          = {APS311407},
  pmc          = {PMC7845765},
  pmid         = {33552749},
  pubmodel     = {Electronic-eCollection},
  pubstate     = {epublish},
  revised      = {2021-02-10},
}

@Article{Cunha2020,
  author                 = {Cunha, Aureliano C. and Santos, Renato A. Corrêa Dos and Riaño-Pachon, Diego Mauricio and Squina, Fábio M. and Oliveira, Juliana V. C. and Goldman, Gustavo H. and Souza, Aline T. and Gomes, Lorena S. and Godoy-Santos, Fernanda and Teixeira, Janaina A. and Faria-Oliveira, Fábio and Rosse, Izinara C. and Castro, Ieso M. and Lucas, Cândida and Brandão, Rogelio L.},
  journal                = {Genetics and molecular biology},
  title                  = {Draft genome sequence of Wickerhamomyces anomalus LBCM1105, isolated from cachaça fermentation.},
  year                   = {2020},
  pages                  = {e20190122},
  volume                 = {43},
  electronic-issn        = {1678-4685},
  linking-issn           = {1415-4757},
  print-issn             = {1415-4757},
  abstract               = {Wickerhamomyces anomalus LBCM1105 is a yeast isolated from cachaça distillery fermentation vats, notable for exceptional glycerol consumption ability. We report its draft genome with 20.5x in-depth coverage and around 90% extension and completeness. It harbors the sequences of proteins involved in glycerol transport and metabolism.},
  article-doi            = {10.1590/1678-4685-GMB-2019-0122},
  article-pii            = {S1415-47572020000500802},
  electronic-publication = {20200608},
  history                = {2020/06/09 06:01 [medline]},
  issue                  = {3},
  language               = {eng},
  location-id            = {e20190122},
  nlm-unique-id          = {100883590},
  owner                  = {NLM},
  publication-status     = {epublish},
  revised                = {20200928},
  source                 = {Genet Mol Biol. 2020 Jun 8;43(3):e20190122. doi: 10.1590/1678-4685-GMB-2019-0122. eCollection 2020.},
  status                 = {PubMed-not-MEDLINE},
  title-abbreviation     = {Genet Mol Biol},
}

@Article{Hurtado2019,
  author                 = {Hurtado, Fernando Manuel Matias and Pinto, Maísa de Siqueira and Oliveira, Perla Novais de and Riaño-Pachón, Diego Mauricio and Inocente, Laura Beatriz and Carrer, Helaine},
  journal                = {Genes},
  title                  = {Analysis of NAC Domain Transcription Factor Genes of Tectona grandis L.f. Involved in Secondary Cell Wall Deposition.},
  year                   = {2019},
  month                  = {Dec},
  volume                 = {11},
  abstract               = {NAC proteins are one of the largest families of plant-specific transcription factors (TFs). They regulate diverse complex biological processes, including secondary xylem differentiation and wood formation. Recent genomic and transcriptomic studies of Tectona grandis L.f. (teak), one of the most valuable hardwood trees in the world, have allowed identification and analysis of developmental genes. In the present work, T. grandis NAC genes were identified and analyzed regarding to their evolution and expression profile during wood formation. We analyzed the recently published T. grandis genome, and identified 130 NAC proteins that are coded by 107 gene loci. These proteins were classified into 23 clades of the NAC family, together with Populus, Eucalyptus, and Arabidopsis. Data on transcript expression revealed specific temporal and spatial expression patterns for the majority of teak NAC genes. RT-PCR indicated expression of VND genes (Tg11g04450-VND2 and Tg15g08390-VND4) related to secondary cell wall formation in xylem vessels of 16-year-old juvenile trees. Our findings open a way to further understanding of NAC transcription factor genes in T. grandis wood biosynthesis, while they are potentially useful for future studies aiming to improve biomass and wood quality using biotechnological approaches.},
  article-doi            = {10.3390/genes11010020},
  article-pii            = {genes-11-00020},
  completed              = {20200601},
  electronic-issn        = {2073-4425},
  electronic-publication = {20191223},
  history                = {2020/06/02 06:00 [medline]},
  issue                  = {1},
  keywords               = {Arabidopsis/genetics, Cell Wall/genetics, Eucalyptus/genetics, Gene Expression Profiling/methods, Gene Expression Regulation, Plant/genetics, Genes, Lamiaceae/*genetics, Plant Proteins/genetics, Populus/genetics, Transcription Factors/*genetics/*metabolism, Transcriptome/genetics, Wood/genetics/metabolism, Xylem/genetics/metabolism, *secondary growth, *tropical tree, *wood formation},
  language               = {eng},
  linking-issn           = {2073-4425},
  location-id            = {20},
  nlm-unique-id          = {101551097},
  owner                  = {NLM},
  publication-status     = {epublish},
  registry-number        = {0 (Transcription Factors)},
  revised                = {20200601},
  source                 = {Genes (Basel). 2019 Dec 23;11(1):20. doi: 10.3390/genes11010020.},
  status                 = {MEDLINE},
  subset                 = {IM},
  termowner              = {NOTNLM},
  title-abbreviation     = {Genes (Basel)},
}

@Article{LloydEvans2019,
  author                 = {Lloyd Evans, Dyfed and Hlongwane, Thandekile Thandiwe and Joshi, Shailesh V. and Riaño Pachón, Diego Mauricio},
  journal                = {PeerJ},
  title                  = {The sugarcane mitochondrial genome: assembly, phylogenetics and transcriptomics.},
  year                   = {2019},
  pages                  = {e7558},
  volume                 = {7},
  electronic-issn        = {2167-8359},
  linking-issn           = {2167-8359},
  print-issn             = {2167-8359},
  abstract               = {BACKGROUND: Chloroplast genomes provide insufficient phylogenetic information to distinguish between closely related sugarcane cultivars, due to the recent origin of many cultivars and the conserved sequence of the chloroplast. In comparison, the mitochondrial genome of plants is much larger and more plastic and could contain increased phylogenetic signals. We assembled a consensus reference mitochondrion with Illumina TruSeq synthetic long reads and Oxford Nanopore Technologies MinION long reads. Based on this assembly we also analyzed the mitochondrial transcriptomes of sugarcane and sorghum and improved the annotation of the sugarcane mitochondrion as compared with other species. METHODS: Mitochondrial genomes were assembled from genomic read pools using a bait and assemble methodology. The mitogenome was exhaustively annotated using BLAST and transcript datasets were mapped with HISAT2 prior to analysis with the Integrated Genome Viewer. RESULTS: The sugarcane mitochondrion is comprised of two independent chromosomes, for which there is no evidence of recombination. Based on the reference assembly from the sugarcane cultivar SP80-3280 the mitogenomes of four additional cultivars (R570, LCP85-384, RB72343 and SP70-1143) were assembled (with the SP70-1143 assembly utilizing both genomic and transcriptomic data). We demonstrate that the sugarcane plastome is completely transcribed and we assembled the chloroplast genome of SP80-3280 using transcriptomic data only. Phylogenomic analysis using mitogenomes allow closely related sugarcane cultivars to be distinguished and supports the discrimination between Saccharum officinarum and Saccharum cultum as modern sugarcane's female parent. From whole chloroplast comparisons, we demonstrate that modern sugarcane arose from a limited number of Saccharum cultum female founders. Transcriptomic and spliceosomal analyses reveal that the two chromosomes of the sugarcane mitochondrion are combined at the transcript level and that splice sites occur more frequently within gene coding regions than without. We reveal one confirmed and one potential cytoplasmic male sterility (CMS) factor in the sugarcane mitochondrion, both of which are transcribed. CONCLUSION: Transcript processing in the sugarcane mitochondrion is highly complex with diverse splice events, the majority of which span the two chromosomes. PolyA baited transcripts are consistent with the use of polyadenylation for transcript degradation. For the first time we annotate two CMS factors within the sugarcane mitochondrion and demonstrate that sugarcane possesses all the molecular machinery required for CMS and rescue. A mechanism of cross-chromosomal splicing based on guide RNAs is proposed. We also demonstrate that mitogenomes can be used to perform phylogenomic studies on sugarcane cultivars.},
  article-doi            = {10.7717/peerj.7558},
  article-pii            = {7558},
  electronic-publication = {20190924},
  history                = {2019/10/04 06:01 [medline]},
  keywords               = {Cytoplasmic male sterility, Mitochondria, Phylogenetics, Plastomes, RNA splicing, Saccharum cultum, Sugarcane, Sugarcane origins},
  language               = {eng},
  location-id            = {e7558},
  nlm-unique-id          = {101603425},
  owner                  = {NLM},
  publication-status     = {epublish},
  revised                = {20201001},
  second-id              = {Dryad/10.5061/dryad.634d24h},
  source                 = {PeerJ. 2019 Sep 24;7:e7558. doi: 10.7717/peerj.7558. eCollection 2019.},
  status                 = {PubMed-not-MEDLINE},
  termowner              = {NOTNLM},
  title-abbreviation     = {PeerJ},
}

@Article{Fernandes2019,
  author                 = {Fernandes, Bruna S. and Dias, Oscar and Costa, Gisela and Kaupert Neto, Antonio A. and Resende, Tiago F. C. and Oliveira, Juliana V. C. and Riaño-Pachón, Diego Mauricio and Zaiat, Marcelo and Pradella, José G. C. and Rocha, Isabel},
  journal                = {BMC biotechnology},
  title                  = {Genome-wide sequencing and metabolic annotation of Pythium irregulare CBS 494.86: understanding Eicosapentaenoic acid production.},
  year                   = {2019},
  month                  = {Jun},
  pages                  = {41},
  volume                 = {19},
  electronic-issn        = {1472-6750},
  linking-issn           = {1472-6750},
  abstract               = {BACKGROUND: Pythium irregulare is an oleaginous Oomycete able to accumulate large amounts of lipids, including Eicosapentaenoic acid (EPA). EPA is an important and expensive dietary supplement with a promising and very competitive market, which is dependent on fish-oil extraction. This has prompted several research groups to study biotechnological routes to obtain specific fatty acids rather than a mixture of various lipids. Moreover, microorganisms can use low cost carbon sources for lipid production, thus reducing production costs. Previous studies have highlighted the production of EPA by P. irregulare, exploiting diverse low cost carbon sources that are produced in large amounts, such as vinasse, glycerol, and food wastewater. However, there is still a lack of knowledge about its biosynthetic pathways, because no functional annotation of any Pythium sp. exists yet. The goal of this work was to identify key genes and pathways related to EPA biosynthesis, in P. irregulare CBS 494.86, by sequencing and performing an unprecedented annotation of its genome, considering the possibility of using wastewater as a carbon source. RESULTS: Genome sequencing provided 17,727 candidate genes, with 3809 of them associated with enzyme code and 945 with membrane transporter proteins. The functional annotation was compared with curated information of oleaginous organisms, understanding amino acids and fatty acids production, and consumption of carbon and nitrogen sources, present in the wastewater. The main features include the presence of genes related to the consumption of several sugars and candidate genes of unsaturated fatty acids production. CONCLUSIONS: The whole metabolic genome presented, which is an unprecedented reconstruction of P. irregulare CBS 494.86, shows its potential to produce value-added products, in special EPA, for food and pharmaceutical industries, moreover it infers metabolic capabilities of the microorganism by incorporating information obtained from literature and genomic data, supplying information of great importance to future work.},
  article-doi            = {10.1186/s12896-019-0529-3},
  article-pii            = {529},
  completed              = {20200113},
  electronic-publication = {20190628},
  history                = {2020/01/14 06:00 [medline]},
  issue                  = {1},
  keywords               = {Dietary Supplements, Eicosapentaenoic Acid/*biosynthesis, Fungal Proteins/*genetics/metabolism, *Gene Expression Regulation, Fungal, Genome, Fungal/*genetics, High-Throughput Nucleotide Sequencing/*methods, Industrial Microbiology/methods, Pythium/*genetics/metabolism, *Eicosapentaenoic acid, *Metabolic annotation, *Pythium irregulare, unsaturated fatty acids, whole-genome sequence},
  language               = {eng},
  location-id            = {41},
  nlm-unique-id          = {101088663},
  owner                  = {NLM},
  publication-status     = {epublish},
  registry-number        = {AAN7QOV9EA (Eicosapentaenoic Acid)},
  revised                = {20200309},
  source                 = {BMC Biotechnol. 2019 Jun 28;19(1):41. doi: 10.1186/s12896-019-0529-3.},
  status                 = {MEDLINE},
  subset                 = {IM},
  termowner              = {NOTNLM},
  title-abbreviation     = {BMC Biotechnol},
}

@Article{Castro2019,
  author                 = {Castro, Juan Camilo and Valdés, Ivan and Gonzalez-García, Laura Natalia and Danies, Giovanna and Cañas, Silvia and Winck, Flavia Vischi and Ñústez, Carlos Eduardo and Restrepo, Silvia and Riaño-Pachón, Diego Mauricio},
  journal                = {Theoretical biology & medical modelling},
  title                  = {Gene regulatory networks on transfer entropy (GRNTE): a novel approach to reconstruct gene regulatory interactions applied to a case study for the plant pathogen Phytophthora infestans.},
  year                   = {2019},
  month                  = {Apr},
  pages                  = {7},
  volume                 = {16},
  electronic-issn        = {1742-4682},
  linking-issn           = {1742-4682},
  abstract               = {BACKGROUND: The increasing amounts of genomics data have helped in the understanding of the molecular dynamics of complex systems such as plant and animal diseases. However, transcriptional regulation, although playing a central role in the decision-making process of cellular systems, is still poorly understood. In this study, we linked expression data with mathematical models to infer gene regulatory networks (GRN). We present a simple yet effective method to estimate transcription factors' GRNs from transcriptional data. METHOD: We defined interactions between pairs of genes (edges in the GRN) as the partial mutual information between these genes that takes into account time and possible lags in time from one gene in relation to another. We call this method Gene Regulatory Networks on Transfer Entropy (GRNTE) and it corresponds to Granger causality for Gaussian variables in an autoregressive model. To evaluate the reconstruction accuracy of our method, we generated several sub-networks from the GRN of the eukaryotic yeast model, Saccharomyces cerevisae. Then, we applied this method using experimental data of the plant pathogen Phytophthora infestans. We evaluated the transcriptional expression levels of 48 transcription factors of P. infestans during its interaction with one moderately resistant and one susceptible cultivar of yellow potato (Solanum tuberosum group Phureja), using RT-qPCR. With these data, we reconstructed the regulatory network of P. infestans during its interaction with these hosts. RESULTS: We first evaluated the performance of our method, based on the transfer entropy (GRNTE), on eukaryotic datasets from the GRNs of the yeast S. cerevisae. Results suggest that GRNTE is comparable with the state-of-the-art methods when the parameters for edge detection are properly tuned. In the case of P. infestans, most of the genes considered in this study, showed a significant change in expression from the onset of the interaction (0 h post inoculum - hpi) to the later time-points post inoculation. Hierarchical clustering of the expression data discriminated two distinct periods during the infection: from 12 to 36 hpi and from 48 to 72 hpi for both the moderately resistant and susceptible cultivars. These distinct periods could be associated with two phases of the life cycle of the pathogen when infecting the host plant: the biotrophic and necrotrophic phases. CONCLUSIONS: Here we presented an algorithmic solution to the problem of network reconstruction in time series data. This analytical perspective makes use of the dynamic nature of time series data as it relates to intrinsically dynamic processes such as transcription regulation, were multiple elements of the cell (e.g., transcription factors) act simultaneously and change over time. We applied the algorithm to study the regulatory network of P. infestans during its interaction with two hosts which differ in their level of resistance to the pathogen. Although the gene expression analysis did not show differences between the two hosts, the results of the GRN analyses evidenced rewiring of the genes' interactions according to the resistance level of the host. This suggests that different regulatory processes are activated in response to different environmental cues. Applications of our methodology showed that it could reliably predict where to place edges in the transcriptional networks and sub-networks. The experimental approach used here can help provide insights on the biological role of these interactions on complex processes such as pathogenicity. The code used is available at https://github.com/jccastrog/GRNTE under GNU general public license 3.0.},
  article-doi            = {10.1186/s12976-019-0103-7},
  article-pii            = {103},
  completed              = {20190802},
  electronic-publication = {20190409},
  history                = {2019/08/03 06:00 [medline]},
  issue                  = {1},
  keywords               = {*Algorithms, *Databases, Genetic, Entropy, Gene Regulatory Networks/*genetics, *Models, Theoretical, Phytophthora infestans/*genetics, *Biological networks, *Entropy, *Gene regulation, *Information theory, *Transcription factors},
  language               = {eng},
  location-id            = {7},
  nlm-unique-id          = {101224383},
  owner                  = {NLM},
  publication-status     = {epublish},
  revised                = {20200225},
  source                 = {Theor Biol Med Model. 2019 Apr 9;16(1):7. doi: 10.1186/s12976-019-0103-7.},
  status                 = {MEDLINE},
  termowner              = {NOTNLM},
  title-abbreviation     = {Theor Biol Med Model},
}

@Article{Fonseca2019,
  author                 = {Fonseca, Bruna Constante and Riaño-Pachón, Diego Mauricio and Guazzaroni, María-Eugenia and Reginatto, Valeria},
  journal                = {Genetics and molecular biology},
  title                  = {Genome sequence of the H2-producing Clostridium beijerinckii strain Br21 isolated from a sugarcane vinasse treatment plant.},
  year                   = {2019},
  month                  = {Jan-Mar},
  pages                  = {139-144},
  volume                 = {42},
  electronic-issn        = {1678-4685},
  linking-issn           = {1415-4757},
  print-issn             = {1415-4757},
  abstract               = {We report on the nearly complete genome sequence of Clostridium beijerinckii strain Br21, formerly isolated from a sugarcarne vinasse wastewater treatment plant. The resulting genome is ca. 5.9 Mbp in length and resembles the size of previously published C. beijerinckii genomes. We annotated the genome sequence and predicted a total of 5323 genes. Strain Br21 has a genetic toolkit that allows it to exploit diverse sugars that are often found after lignocellulosic biomass pretreatment to yield products of commercial interest. Besides the whole set of genes encoding for enzymes underlying hydrogen production, the genome of the new strain includes genes that enable carbon sources conversion into butanol, ethanol, acetic acid, butyric acid, and the chemical block 1,3-propanediol, which is used to obtain polymers. Moreover, the genome of strain Br21 has a higher number of ORFs with predicted beta-glucosidase activity as compared to other C. beijerinckii strains described in the KEGG database. These characteristics make C. beijerinckii strain Br21 a remarkable candidate for direct use in biotechnological processes and attest that it is a potential biocatalyst supplier.},
  article-doi            = {10.1590/1678-4685-GMB-2017-0315},
  article-pii            = {S1415-47572019005003101},
  electronic-publication = {20190131},
  history                = {2019/02/08 06:00 [entrez]},
  issue                  = {1},
  language               = {eng},
  location-id            = {10.1590/1678-4685-GMB-2017-0315 [doi]},
  nlm-unique-id          = {100883590},
  owner                  = {NLM},
  publication-status     = {ppublish},
  revised                = {20200930},
  source                 = {Genet Mol Biol. 2019 Jan-Mar;42(1):139-144. doi: 10.1590/1678-4685-GMB-2017-0315. Epub 2019 Jan 31.},
  status                 = {PubMed-not-MEDLINE},
  title-abbreviation     = {Genet Mol Biol},
}

@Article{Borin2018,
  author                 = {Borin, Gustavo Pagotto and Carazzolle, Marcelo Falsarella and Dos Santos, Renato Augusto Corrêa and Riaño-Pachón, Diego Mauricio and Oliveira, Juliana Velasco de Castro},
  journal                = {Frontiers in bioengineering and biotechnology},
  title                  = {Gene Co-expression Network Reveals Potential New Genes Related to Sugarcane Bagasse Degradation in Trichoderma reesei RUT-30.},
  year                   = {2018},
  pages                  = {151},
  volume                 = {6},
  electronic-issn        = {2296-4185},
  linking-issn           = {2296-4185},
  print-issn             = {2296-4185},
  abstract               = {The biomass-degrading fungus Trichoderma reesei has been considered a model for cellulose degradation, and it is the primary source of the industrial enzymatic cocktails used in second-generation (2G) ethanol production. However, although various studies and advances have been conducted to understand the cellulolytic system and the transcriptional regulation of T. reesei, the whole set of genes related to lignocellulose degradation has not been completely elucidated. In this study, we inferred a weighted gene co-expression network analysis based on the transcriptome dataset of the T. reesei RUT-C30 strain aiming to identify new target genes involved in sugarcane bagasse breakdown. In total, ~70% of all the differentially expressed genes were found in 28 highly connected gene modules. Several cellulases, sugar transporters, and hypothetical proteins coding genes upregulated in bagasse were grouped into the same modules. Among them, a single module contained the most representative core of cellulolytic enzymes (cellobiohydrolase, endoglucanase, β-glucosidase, and lytic polysaccharide monooxygenase). In addition, functional analysis using Gene Ontology (GO) revealed various classes of hydrolytic activity, cellulase activity, carbohydrate binding and cation:sugar symporter activity enriched in these modules. Several modules also showed GO enrichment for transcription factor activity, indicating the presence of transcriptional regulators along with the genes involved in cellulose breakdown and sugar transport as well as other genes encoding proteins with unknown functions. Highly connected genes (hubs) were also identified within each module, such as predicted transcription factors and genes encoding hypothetical proteins. In addition, various hubs contained at least one DNA binding site for the master activator Xyr1 according to our in silico analysis. The prediction of Xyr1 binding sites and the co-expression with genes encoding carbohydrate active enzymes and sugar transporters suggest a putative role of these hubs in bagasse cell wall deconstruction. Our results demonstrate a vast range of new promising targets that merit additional studies to improve the cellulolytic potential of T. reesei strains and to decrease the production costs of 2G ethanol.},
  article-doi            = {10.3389/fbioe.2018.00151},
  electronic-publication = {20181022},
  history                = {2018/11/09 06:01 [medline]},
  keywords               = {2G ethanol, Trichoderma reesei, Xyr1-binding site, enzymatic cocktail, gene co-expression network, sugarcane bagasse},
  language               = {eng},
  location-id            = {151},
  nlm-unique-id          = {101632513},
  owner                  = {NLM},
  publication-status     = {epublish},
  revised                = {20200929},
  source                 = {Front Bioeng Biotechnol. 2018 Oct 22;6:151. doi: 10.3389/fbioe.2018.00151. eCollection 2018.},
  status                 = {PubMed-not-MEDLINE},
  termowner              = {NOTNLM},
  title-abbreviation     = {Front Bioeng Biotechnol},
}

@Article{Gouvea2018,
  author                 = {de Gouvêa, Paula Fagundes and Bernardi, Aline Vianna and Gerolamo, Luis Eduardo and de Souza Santos, Emerson and Riaño-Pachón, Diego Mauricio and Uyemura, Sergio Akira and Dinamarco, Taisa Magnani},
  journal                = {BMC genomics},
  title                  = {Transcriptome and secretome analysis of Aspergillus fumigatus in the presence of sugarcane bagasse.},
  year                   = {2018},
  month                  = {Apr},
  pages                  = {232},
  volume                 = {19},
  abstract               = {BACKGROUND: Sugarcane bagasse has been proposed as a lignocellulosic residue for second-generation ethanol (2G) produced by breaking down biomass into fermentable sugars. The enzymatic cocktails for biomass degradation are mostly produced by fungi, but low cost and high efficiency can consolidate 2G technologies. A. fumigatus plays an important role in plant biomass degradation capabilities and recycling. To gain more insight into the divergence in gene expression during steam-exploded bagasse (SEB) breakdown, this study profiled the transcriptome of A. fumigatus by RNA sequencing to compare transcriptional profiles of A. fumigatus grown on media containing SEB or fructose as the sole carbon source. Secretome analysis was also performed using SDS-PAGE and LC-MS/MS. RESULTS: The maximum activities of cellulases (0.032 U mL-1), endo-1,4-β--xylanase (10.82 U mL-1) and endo-1,3-β glucanases (0.77 U mL-1) showed that functional CAZymes (carbohydrate-active enzymes) were secreted in the SEB culture conditions. Correlations between transcriptome and secretome data identified several CAZymes in A. fumigatus. Particular attention was given to CAZymes related to lignocellulose degradation and sugar transporters. Genes encoding glycoside hydrolase classes commonly expressed during the breakdown of cellulose, such as GH-5, 6, 7, 43, 45, and hemicellulose, such as GH-2, 10, 11, 30, 43, were found to be highly expressed in SEB conditions. Lytic polysaccharide monooxygenases (LPMO) classified as auxiliary activity families AA9 (GH61), CE (1, 4, 8, 15, 16), PL (1, 3, 4, 20) and GT (1, 2, 4, 8, 20, 35, 48) were also differentially expressed in this condition. Similarly, the most important enzymes related to biomass degradation, including endoxylanases, xyloglucanases, β-xylosidases, LPMOs, α-arabinofuranosidases, cellobiohydrolases, endoglucanases and β-glucosidases, were also identified in the secretome. CONCLUSIONS: This is the first report of a transcriptome and secretome experiment of Aspergillus fumigatus in the degradation of pretreated sugarcane bagasse. The results suggest that this strain employs important strategies for this complex degradation process. It was possible to identify a set of genes and proteins that might be applied in several biotechnology fields. This knowledge can be exploited for the improvement of 2G ethanol production by the rational design of enzymatic cocktails.},
  article-doi            = {10.1186/s12864-018-4627-8},
  article-pii            = {4627},
  completed              = {20181211},
  electronic-issn        = {1471-2164},
  electronic-publication = {20180403},
  grantno                = {2014/10466-0/Fundação de Amparo à Pesquisa do Estado de São Paulo/},
  history                = {2018/12/12 06:00 [medline]},
  issue                  = {1},
  keywords               = {Aspergillus fumigatus/genetics/*growth & development/metabolism, Cellulases/genetics/metabolism, Cellulose/*chemistry, Chromatography, Liquid, Fructose/chemistry, Fungal Proteins/*genetics/*metabolism, Gene Expression Profiling/*methods, Glucan Endo-1, 3-beta-D-Glucosidase/genetics/metabolism, Glycoside Hydrolases/genetics/metabolism, Saccharum/metabolism, Sequence Analysis, RNA/methods, Tandem Mass Spectrometry, Xylosidases/genetics/metabolism, Aspergillus fumigatus, CAZymes, Lignocellulose breakdown, RNA-Seq, Secretome, Sugarcane bagasse},
  language               = {eng},
  linking-issn           = {1471-2164},
  location-id            = {232},
  nlm-unique-id          = {100965258},
  owner                  = {NLM},
  publication-status     = {epublish},
  registry-number        = {EC 3.2.1.39 (Glucan Endo-1,3-beta-D-Glucosidase)},
  revised                = {20181211},
  source                 = {BMC Genomics. 2018 Apr 3;19(1):232. doi: 10.1186/s12864-018-4627-8.},
  status                 = {MEDLINE},
  subset                 = {IM},
  termowner              = {NOTNLM},
  title-abbreviation     = {BMC Genomics},
}

@Article{Mello2017,
  author                 = {Mello, Bruno L. and Alessi, Anna M. and Riaño-Pachón, Diego Mauricio and deAzevedo, Eduardo R. and Guimarães, Francisco E. G. and Espirito Santo, Melissa C. and McQueen-Mason, Simon and Bruce, Neil C. and Polikarpov, Igor},
  journal                = {Biotechnology for biofuels},
  title                  = {Targeted metatranscriptomics of compost-derived consortia reveals a GH11 exerting an unusual exo-1,4-β-xylanase activity.},
  year                   = {2017},
  pages                  = {254},
  volume                 = {10},
  electronic-issn        = {1754-6834},
  linking-issn           = {1754-6834},
  print-issn             = {1754-6834},
  abstract               = {BACKGROUND: Using globally abundant crop residues as a carbon source for energy generation and renewable chemicals production stand out as a promising solution to reduce current dependency on fossil fuels. In nature, such as in compost habitats, microbial communities efficiently degrade the available plant biomass using a diverse set of synergistic enzymes. However, deconstruction of lignocellulose remains a challenge for industry due to recalcitrant nature of the substrate and the inefficiency of the enzyme systems available, making the economic production of lignocellulosic biofuels difficult. Metatranscriptomic studies of microbial communities can unveil the metabolic functions employed by lignocellulolytic consortia and identify novel biocatalysts that could improve industrial lignocellulose conversion. RESULTS: In this study, a microbial community from compost was grown in minimal medium with sugarcane bagasse sugarcane bagasse as the sole carbon source. Solid-state nuclear magnetic resonance was used to monitor lignocellulose degradation; analysis of metatranscriptomic data led to the selection and functional characterization of several target genes, revealing the first glycoside hydrolase from Carbohydrate Active Enzyme family 11 with exo-1,4-β-xylanase activity. The xylanase crystal structure was resolved at 1.76 Å revealing the structural basis of exo-xylanase activity. Supplementation of a commercial cellulolytic enzyme cocktail with the xylanase showed improvement in Avicel hydrolysis in the presence of inhibitory xylooligomers. CONCLUSIONS: This study demonstrated that composting microbiomes continue to be an excellent source of biotechnologically important enzymes by unveiling the diversity of enzymes involved in in situ lignocellulose degradation.},
  article-doi            = {10.1186/s13068-017-0944-4},
  article-pii            = {944},
  electronic-publication = {20171102},
  grantno                = {BB/I018492/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom},
  history                = {2017/11/10 06:01 [medline]},
  keywords               = {Bioethanol, Compost, Lignocellulose, Metatranscriptomics, Microbial community, Xylanase},
  language               = {eng},
  location-id            = {254},
  nlm-unique-id          = {101316935},
  owner                  = {NLM},
  publication-status     = {epublish},
  revised                = {20210109},
  source                 = {Biotechnol Biofuels. 2017 Nov 2;10:254. doi: 10.1186/s13068-017-0944-4. eCollection 2017.},
  status                 = {PubMed-not-MEDLINE},
  termowner              = {NOTNLM},
  title-abbreviation     = {Biotechnol Biofuels},
}

@Article{Contesini2017,
  author                 = {Contesini, Fabiano Jares and Liberato, Marcelo Vizoná and Rubio, Marcelo Ventura and Calzado, Felipe and Zubieta, Mariane Paludetti and Riaño-Pachón, Diego Mauricio and Squina, Fabio Marcio and Bracht, Fabricio and Skaf, Munir S. and Damasio, André Ricardo},
  journal                = {Biochimica et biophysica acta. Proteins and proteomics},
  title                  = {Structural and functional characterization of a highly secreted α-l-arabinofuranosidase (GH62) from Aspergillus nidulans grown on sugarcane bagasse.},
  year                   = {2017},
  month                  = {Dec},
  pages                  = {1758-1769},
  volume                 = {1865},
  linking-issn           = {1570-9639},
  print-issn             = {1570-9639},
  abstract               = {Carbohydrate-Active Enzymes are key enzymes for biomass-to-bioproducts conversion. α-l-Arabinofuranosidases that belong to the Glycoside Hydrolase family 62 (GH62) have important applications in biofuel production from plant biomass by hydrolyzing arabinoxylans, found in both the primary and secondary cell walls of plants. In this work, we identified a GH62 α-l-arabinofuranosidase (AnAbf62A(wt)) that was highly secreted when Aspergillus nidulans was cultivated on sugarcane bagasse. The gene AN7908 was cloned and transformed in A. nidulans for homologous production of AnAbf62A(wt), and we confirmed that the enzyme is N-glycosylated at asparagine 83 by mass spectrometry analysis. The enzyme was also expressed in Escherichia coli and the studies of circular dichroism showed that the melting temperature and structural profile of AnAbf62A(wt) and the non-glycosylated enzyme from E. coli (AnAbf62A(deglyc)) were highly similar. In addition, the designed glycomutant AnAbf62A(N83Q) presented similar patterns of secretion and activity to the AnAbf62A(wt), indicating that the N-glycan does not influence the properties of this enzyme. The crystallographic structure of AnAbf62A(deglyc) was obtained and the 1.7Å resolution model showed a five-bladed β-propeller fold, which is conserved in family GH62. Mutants AnAbf62A(Y312F) and AnAbf62A(Y312S) showed that Y312 was an important substrate-binding residue. Molecular dynamics simulations indicated that the loop containing Y312 could access different conformations separated by moderately low energy barriers. One of these conformations, comprising a local minimum, is responsible for placing Y312 in the vicinity of the arabinose glycosidic bond, and thus, may be important for catalytic efficiency.},
  address                = {Netherlands},
  article-doi            = {10.1016/j.bbapap.2017.09.001},
  article-pii            = {S1570-9639(17)30209-1},
  completed              = {20171221},
  electronic-publication = {20170908},
  history                = {2017/09/12 06:00 [entrez]},
  issue                  = {12},
  keywords               = {Aspergillus nidulans/*enzymology/growth & development, Cellulose/*pharmacology, Crystallography, Glycoside Hydrolases/*chemistry/physiology, Glycosylation, Molecular Dynamics Simulation, *Arabinoxylan, *Aspergillus nidulans, *GH62, *N-glycosylation, *α-l-Arabinofuranosidase},
  language               = {eng},
  location-id            = {10.1016/j.bbapap.2017.09.001 [doi]},
  nlm-unique-id          = {101731734},
  owner                  = {NLM},
  publication-status     = {ppublish},
  registry-number        = {EC 3.2.1.55 (alpha-N-arabinofuranosidase)},
  revised                = {20180917},
  source                 = {Biochim Biophys Acta Proteins Proteom. 2017 Dec;1865(12):1758-1769. doi: 10.1016/j.bbapap.2017.09.001. Epub 2017 Sep 8.},
  status                 = {MEDLINE},
  subset                 = {IM},
  termowner              = {NOTNLM},
  title-abbreviation     = {Biochim Biophys Acta Proteins Proteom},
}

@Article{Manfiolli2017,
  author                 = {Manfiolli, Adriana Oliveira and de Castro, Patrícia Alves and Dos Reis, Thaila Fernanda and Dolan, Stephen and Doyle, Sean and Jones, Gary and Riaño Pachón, Diego Mauricio and Ulaş, Mevlüt and Noble, Luke M. and Mattern, Derek J. and Brakhage, Axel A. and Valiante, Vito and Silva-Rocha, Rafael and Bayram, Ozgur and Goldman, Gustavo H.},
  journal                = {Cellular microbiology},
  title                  = {Aspergillus fumigatus protein phosphatase PpzA is involved in iron assimilation, secondary metabolite production, and virulence.},
  year                   = {2017},
  month                  = {Dec},
  volume                 = {19},
  electronic-issn        = {1462-5822},
  linking-issn           = {1462-5814},
  abstract               = {Metal restriction imposed by mammalian hosts during an infection is a common mechanism of defence to reduce or avoid the pathogen infection. Metals are essential for organism survival due to its involvement in several biological processes. Aspergillus fumigatus causes invasive aspergillosis, a disease that typically manifests in immunocompromised patients. A. fumigatus PpzA, the catalytic subunit of protein phosphatase Z (PPZ), has been recently identified as associated with iron assimilation. A. fumigatus has 2 high-affinity mechanisms of iron acquisition during infection: reductive iron assimilation and siderophore-mediated iron uptake. It has been shown that siderophore production is important for A. fumigatus virulence, differently to the reductive iron uptake system. Transcriptomic and proteomic comparisons between ∆ppzA and wild-type strains under iron starvation showed that PpzA has a broad influence on genes involved in secondary metabolism. Liquid chromatography-mass spectrometry under standard and iron starvation conditions confirmed that the ΔppzA mutant had reduced production of pyripyropene A, fumagillin, fumiquinazoline A, triacetyl-fusarinine C, and helvolic acid. The ΔppzA was shown to be avirulent in a neutropenic murine model of invasive pulmonary aspergillosis. PpzA plays an important role at the interface between iron starvation, regulation of SM production, and pathogenicity in A. fumigatus.},
  address                = {England},
  article-doi            = {10.1111/cmi.12770},
  completed              = {20180619},
  electronic-publication = {20170817},
  history                = {2017/07/29 06:00 [entrez]},
  issue                  = {12},
  keywords               = {Animals, Aspergillus fumigatus/*enzymology/genetics/metabolism/*pathogenicity, Chromatography, Liquid, Disease Models, Animal, Gene Deletion, Gene Expression Profiling, Invasive Pulmonary Aspergillosis/microbiology/pathology, Iron/*metabolism, Mass Spectrometry, Metabolomics, Mice, Phosphoprotein Phosphatases/genetics/*metabolism, Proteome/analysis, *Secondary Metabolism, Virulence},
  language               = {eng},
  location-id            = {10.1111/cmi.12770 [doi]},
  nlm-unique-id          = {100883691},
  owner                  = {NLM},
  publication-status     = {ppublish},
  registry-number        = {EC 3.1.3.16 (Phosphoprotein Phosphatases)},
  revised                = {20201209},
  source                 = {Cell Microbiol. 2017 Dec;19(12). doi: 10.1111/cmi.12770. Epub 2017 Aug 17.},
  status                 = {MEDLINE},
  subset                 = {IM},
  title-abbreviation     = {Cell Microbiol},
}

@Article{RianoPachon2017,
  author                 = {Riaño-Pachón, Diego Mauricio and Mattiello, Lucia},
  journal                = {F1000Research},
  title                  = {Draft genome sequencing of the sugarcane hybrid SP80-3280.},
  year                   = {2017},
  pages                  = {861},
  volume                 = {6},
  electronic-issn        = {2046-1402},
  linking-issn           = {2046-1402},
  print-issn             = {2046-1402},
  abstract               = {Sugarcane commercial cultivar SP80-3280 has been used as a model for genomic analyses in Brazil. Here we present a draft genome sequence employing Illumina TruSeq Synthetic Long reads. The dataset is available from NCBI BioProject with accession PRJNA272769.},
  article-doi            = {10.12688/f1000research.11859.2},
  electronic-publication = {20170609},
  history                = {2017/07/20 06:01 [medline]},
  keywords               = {genomics, long reads, polyploid, sugarcane},
  language               = {eng},
  location-id            = {861},
  nlm-unique-id          = {101594320},
  owner                  = {NLM},
  publication-status     = {epublish},
  revised                = {20191120},
  source                 = {F1000Res. 2017 Jun 9;6:861. doi: 10.12688/f1000research.11859.2. eCollection 2017.},
  status                 = {PubMed-not-MEDLINE},
  termowner              = {NOTNLM},
  title-abbreviation     = {F1000Res},
}

@Article{Nobile2017,
  author                 = {Nobile, Paula Macedo and Bottcher, Alexandra and Mayer, Juliana L. S. and Brito, Michael S. and Dos Anjos, Ivan A. and Landell, Marcos Guimarães de Andrade and Vicentini, Renato and Creste, Silvana and Riaño-Pachón, Diego Mauricio and Mazzafera, Paulo},
  journal                = {Molecular genetics and genomics : MGG},
  title                  = {Identification, classification and transcriptional profiles of dirigent domain-containing proteins in sugarcane.},
  year                   = {2017},
  month                  = {Dec},
  pages                  = {1323-1340},
  volume                 = {292},
  abstract               = {Dirigent (DIR) proteins, encoded by DIR genes, are referred to as "dirigent" because they direct the outcome of the coupling of the monolignol coniferyl alcohol into (+) or (-) pinoresinol, the first intermediates in the enantiocomplementary pathways for lignan biosynthesis. DIR domain-containing or DIR-like proteins are, thus, termed for not having a clear characterization. A transcriptome- and genome-wide survey of DIR domain-containing proteins in sugarcane was carried out, in addition to phylogenetic, physicochemical and transcriptional analyses. A total of 120 non-redundant sequences containing the DIR domain were identified and classified into 64 groups according to phylogenetic and sequence alignment analyses. In silico analysis of transcript abundance showed that these sequences are expressed at low levels in leaves and genes in the same phylogenetic clade have similar expression patterns. Expression analysis of ShDIR1-like transcripts in the culm internodes of sugarcane demonstrates their abundance in mature internodes, their induction by nitrogen fertilization and their predominant expression in cells that have a lignified secondary cell wall, such as vascular bundles of young internodes and parenchymal cells of the pith of mature internodes. Due to the lack of information about the functional role of DIR in plants, a possible relationship is discussed between the ShDIR1-like transcriptional profile and cell wall development in parenchyma cells of sugarcane culm, which typically accumulates large amounts of sucrose. The number of genes encoding the DIR domain-containing proteins in sugarcane is intriguing and is an indication per se that these proteins may have an important metabolic role and thus deserve to be better studied.},
  address                = {Germany},
  article-doi            = {10.1007/s00438-017-1349-6},
  article-pii            = {10.1007/s00438-017-1349-6},
  completed              = {20171124},
  electronic-issn        = {1617-4623},
  electronic-publication = {20170711},
  history                = {2017/07/13 06:00 [entrez]},
  issue                  = {6},
  keywords               = {*Gene Expression Profiling, In Situ Hybridization, Phylogeny, Plant Proteins/chemistry/genetics/*metabolism, Protein Conformation, Saccharum/*metabolism, *Transcription, Genetic, Lignan, Protein homology modeling, Saccharum spp., Transcriptome- and genome-wide survey},
  language               = {eng},
  linking-issn           = {1617-4623},
  location-id            = {10.1007/s00438-017-1349-6 [doi]},
  nlm-unique-id          = {101093320},
  owner                  = {NLM},
  publication-status     = {ppublish},
  registry-number        = {0 (Plant Proteins)},
  revised                = {20200306},
  source                 = {Mol Genet Genomics. 2017 Dec;292(6):1323-1340. doi: 10.1007/s00438-017-1349-6. Epub 2017 Jul 11.},
  status                 = {MEDLINE},
  subset                 = {IM},
  termowner              = {NOTNLM},
  title-abbreviation     = {Mol Genet Genomics},
}

@Article{Borin2017,
  author                 = {Borin, Gustavo Pagotto and Sanchez, Camila Cristina and de Santana, Eliane Silva and Zanini, Guilherme Keppe and Dos Santos, Renato Augusto Corrêa and de Oliveira Pontes, Angélica and de Souza, Aline Tieppo and Dal'Mas, Roberta Maria Menegaldo Tavares Soares and Riaño-Pachón, Diego Mauricio and Goldman, Gustavo Henrique and Oliveira, Juliana Velasco de Castro},
  journal                = {BMC genomics},
  title                  = {Comparative transcriptome analysis reveals different strategies for degradation of steam-exploded sugarcane bagasse by Aspergillus niger and Trichoderma reesei.},
  year                   = {2017},
  month                  = {Jun},
  pages                  = {501},
  volume                 = {18},
  electronic-issn        = {1471-2164},
  linking-issn           = {1471-2164},
  abstract               = {BACKGROUND: Second generation (2G) ethanol is produced by breaking down lignocellulosic biomass into fermentable sugars. In Brazil, sugarcane bagasse has been proposed as the lignocellulosic residue for this biofuel production. The enzymatic cocktails for the degradation of biomass-derived polysaccharides are mostly produced by fungi, such as Aspergillus niger and Trichoderma reesei. However, it is not yet fully understood how these microorganisms degrade plant biomass. In order to identify transcriptomic changes during steam-exploded bagasse (SEB) breakdown, we conducted a RNA-seq comparative transcriptome profiling of both fungi growing on SEB as carbon source. RESULTS: Particular attention was focused on CAZymes, sugar transporters, transcription factors (TFs) and other proteins related to lignocellulose degradation. Although genes coding for the main enzymes involved in biomass deconstruction were expressed by both fungal strains since the beginning of the growth in SEB, significant differences were found in their expression profiles. The expression of these enzymes is mainly regulated at the transcription level, and A. niger and T. reesei also showed differences in TFs content and in their expression. Several sugar transporters that were induced in both fungal strains could be new players on biomass degradation besides their role in sugar uptake. Interestingly, our findings revealed that in both strains several genes that code for proteins of unknown function and pro-oxidant, antioxidant, and detoxification enzymes were induced during growth in SEB as carbon source, but their specific roles on lignocellulose degradation remain to be elucidated. CONCLUSIONS: This is the first report of a time-course experiment monitoring the degradation of pretreated bagasse by two important fungi using the RNA-seq technology. It was possible to identify a set of genes that might be applied in several biotechnology fields. The data suggest that these two microorganisms employ different strategies for biomass breakdown. This knowledge can be exploited for the rational design of enzymatic cocktails and 2G ethanol production improvement.},
  article-doi            = {10.1186/s12864-017-3857-5},
  article-pii            = {3857},
  completed              = {20180226},
  electronic-publication = {20170630},
  history                = {2018/02/27 06:00 [medline]},
  issue                  = {1},
  keywords               = {Aspergillus niger/genetics/*metabolism/physiology, Biomass, Cellulose/*metabolism, Fungal Proteins/genetics/metabolism, *Gene Expression Profiling, Lignin/metabolism, Saccharum/*chemistry/*microbiology, Sequence Analysis, RNA, *Steam, Trichoderma/genetics/*metabolism/physiology, *Aspergillus niger, *CAZymes, *RNA-seq, *Sugarcane bagasse, *Transcription factors, *Transporters, *Trichoderma reesei},
  language               = {eng},
  location-id            = {501},
  nlm-unique-id          = {100965258},
  owner                  = {NLM},
  publication-status     = {epublish},
  registry-number        = {9006-97-7 (bagasse)},
  revised                = {20201209},
  source                 = {BMC Genomics. 2017 Jun 30;18(1):501. doi: 10.1186/s12864-017-3857-5.},
  status                 = {MEDLINE},
  subset                 = {IM},
  termowner              = {NOTNLM},
  title-abbreviation     = {BMC Genomics},
}

@Article{Mandelli2017,
  author                 = {Mandelli, F. and Couger, M. B. and Paixão, D. A. A. and Machado, C. B. and Carnielli, C. M. and Aricetti, J. A. and Polikarpov, I. and Prade, R. and Caldana, C. and Paes Leme, A. F. and Mercadante, A. Z. and Riaño-Pachón, Diego Mauricio and Squina, Fabio Marcio},
  journal                = {Extremophiles : life under extreme conditions},
  title                  = {Thermal adaptation strategies of the extremophile bacterium Thermus filiformis based on multi-omics analysis.},
  year                   = {2017},
  month                  = {Jul},
  pages                  = {775-788},
  volume                 = {21},
  abstract               = {Thermus filiformis is an aerobic thermophilic bacterium isolated from a hot spring in New Zealand. The experimental study of the mechanisms of thermal adaptation is important to unveil response strategies of the microorganism to stress. In this study, the main pathways involved on T. filiformis thermoadaptation, as well as, thermozymes with potential biotechnological applications were revealed based on omics approaches. The strategy adopted in this study disclosed that pathways related to the carbohydrate metabolism were affected in response to thermoadaptation. High temperatures triggered oxidative stress, leading to repression of genes involved in glycolysis and the tricarboxylic acid cycle. During heat stress, the glucose metabolism occurred predominantly via the pentose phosphate pathway instead of the glycolysis pathway. Other processes, such as protein degradation, stringent response, and duplication of aminoacyl-tRNA synthetases, were also related to T. filiformis thermoadaptation. The heat-shock response influenced the carotenoid profile of T. filiformis, favoring the synthesis of thermozeaxanthins and thermobiszeaxanthins, which are related to membrane stabilization at high temperatures. Furthermore, antioxidant enzymes correlated with free radical scavenging, including superoxide dismutase, catalase and peroxidase, and metabolites, such as oxaloacetate and α-ketoglutarate, were accumulated at 77 °C.},
  address                = {Germany},
  article-doi            = {10.1007/s00792-017-0942-2},
  article-pii            = {10.1007/s00792-017-0942-2},
  completed              = {20180326},
  electronic-issn        = {1433-4909},
  electronic-publication = {20170512},
  history                = {2017/05/14 06:00 [entrez]},
  issue                  = {4},
  keywords               = {*Adaptation, Physiological, Extremophiles/*physiology, Hot Temperature, Mass Spectrometry, Metabolomics, Proteomics, Thermus/*physiology, Transcriptome, Peroxyl radical scavenging activity, Thermozeaxanthins, Transcriptomics},
  language               = {eng},
  linking-issn           = {1431-0651},
  location-id            = {10.1007/s00792-017-0942-2 [doi]},
  nlm-unique-id          = {9706854},
  owner                  = {NLM},
  publication-status     = {ppublish},
  revised                = {20181113},
  source                 = {Extremophiles. 2017 Jul;21(4):775-788. doi: 10.1007/s00792-017-0942-2. Epub 2017 May 12.},
  status                 = {MEDLINE},
  subset                 = {S},
  termowner              = {NOTNLM},
  title-abbreviation     = {Extremophiles},
}

@Article{AugustoCorreaDosSantos2017,
  author             = {Augusto Corrêa Dos Santos, Renato and Goldman, Gustavo Henrique and Riaño-Pachón, Diego Mauricio},
  journal            = {Bioinformatics (Oxford, England)},
  title              = {ploidyNGS: visually exploring ploidy with Next Generation Sequencing data.},
  year               = {2017},
  month              = {Aug},
  pages              = {2575-2576},
  volume             = {33},
  electronic-issn    = {1367-4811},
  linking-issn       = {1367-4803},
  abstract           = {SUMMARY: ploidyNGS is a model-free, open source tool to visualize and explore ploidy levels in a newly sequenced genome, exploiting short read data. We tested ploidyNGS using both simulated and real NGS data of the model yeast Saccharomyces cerevisiae. ploidyNGS allows the identification of the ploidy level of a newly sequenced genome in a visual way. AVAILABILITY AND IMPLEMENTATION: ploidyNGS is available under the GNU General Public License (GPL) at https://github.com/diriano/ploidyNGS. ploidyNGS is implemented in Python and R. CONTACT: diriano@gmail.com.},
  address            = {England},
  article-doi        = {10.1093/bioinformatics/btx204},
  article-pii        = {3104472},
  completed          = {20180329},
  history            = {2017/04/07 06:00 [entrez]},
  issue              = {16},
  keywords           = {Genome, Fungal, High-Throughput Nucleotide Sequencing/*methods, *Ploidies, Saccharomyces cerevisiae/genetics, Sequence Analysis, DNA/*methods, *Software},
  language           = {eng},
  location-id        = {10.1093/bioinformatics/btx204 [doi]},
  nlm-unique-id      = {9808944},
  owner              = {NLM},
  publication-status = {ppublish},
  revised            = {20181202},
  source             = {Bioinformatics. 2017 Aug 15;33(16):2575-2576. doi: 10.1093/bioinformatics/btx204.},
  status             = {MEDLINE},
  subset             = {IM},
  title-abbreviation = {Bioinformatics},
}

@Article{DosReis2017,
  author                 = {Dos Reis, Thaila Fernanda and Nitsche, Benjamin M. and de Lima, Pollyne Borborema Almeida and de Assis, Leandro José and Mellado, Laura and Harris, Steven D. and Meyer, Vera and Dos Santos, Renato A. Corrêa and Riaño-Pachón, Diego Mauricio and Ries, Laure Nicolas Annick and Goldman, Gustavo H.},
  journal                = {Scientific reports},
  title                  = {The low affinity glucose transporter HxtB is also involved in glucose signalling and metabolism in Aspergillus nidulans.},
  year                   = {2017},
  month                  = {Mar},
  pages                  = {45073},
  volume                 = {7},
  electronic-issn        = {2045-2322},
  linking-issn           = {2045-2322},
  abstract               = {One of the drawbacks during second-generation biofuel production from plant lignocellulosic biomass is the accumulation of glucose, the preferred carbon source of microorganisms, which causes the repression of hydrolytic enzyme secretion by industrially relevant filamentous fungi. Glucose sensing, subsequent transport and cellular signalling pathways have been barely elucidated in these organisms. This study therefore characterized the transcriptional response of the filamentous fungus Aspergillus nidulans to the presence of high and low glucose concentrations under continuous chemostat cultivation with the aim to identify novel factors involved in glucose sensing and signalling. Several transcription factor- and transporter-encoding genes were identified as being differentially regulated, including the previously characterized glucose and xylose transporter HxtB. HxtB was confirmed to be a low affinity glucose transporter, localizing to the plasma membrane under low- and high-glucose conditions. Furthermore, HxtB was shown to be involved in conidiation-related processes and may play a role in downstream glucose signalling. A gene predicted to encode the protein kinase PskA was also identified as being important for glucose metabolism. This study identified several proteins with predicted roles in glucose metabolic processes and provides a foundation for further investigation into the response of biotechnologically important filamentous fungi to glucose.},
  article-doi            = {10.1038/srep45073},
  article-pii            = {srep45073},
  completed              = {20181112},
  electronic-publication = {20170331},
  history                = {2018/11/13 06:00 [medline]},
  keywords               = {Aspergillus nidulans/drug effects/genetics/*metabolism, *Carbohydrate Metabolism/genetics, Computational Biology/methods, Cyclic AMP/metabolism, Cyclic AMP-Dependent Protein Kinases/metabolism, Gene Deletion, Gene Expression Profiling, Gene Expression Regulation, Fungal/drug effects, Gene Ontology, Glucose/*metabolism/pharmacology, Glucose Transport Proteins, Facilitative/genetics/*metabolism, Phenotype, Protein Binding, Protein Transport, *Signal Transduction/drug effects, Transcription, Genetic, ras Proteins/metabolism},
  language               = {eng},
  location-id            = {45073},
  nlm-unique-id          = {101563288},
  owner                  = {NLM},
  publication-status     = {epublish},
  registry-number        = {IY9XDZ35W2 (Glucose)},
  revised                = {20181113},
  source                 = {Sci Rep. 2017 Mar 31;7:45073. doi: 10.1038/srep45073.},
  status                 = {MEDLINE},
  subset                 = {IM},
  title-abbreviation     = {Sci Rep},
}

@Article{Coutoune2017,
  author                 = {Coutouné, Natalia and Mulato, Aline Tieppo Nogueira and Riaño-Pachón, Diego Mauricio and Oliveira, Juliana Velasco de Castro},
  journal                = {Genome announcements},
  title                  = {Draft Genome Sequence of Saccharomyces cerevisiae Barra Grande (BG-1), a Brazilian Industrial Bioethanol-Producing Strain.},
  year                   = {2017},
  month                  = {Mar},
  volume                 = {5},
  electronic-issn        = {2169-8287},
  print-issn             = {2169-8287},
  abstract               = {Here, we present the draft genome sequence of Saccharomyces cerevisiae BG-1, a Brazilian industrial strain widely used for bioethanol production from sugarcane. The 11.7-Mb genome sequence consists of 216 scaffolds and harbors 5,607 predicted protein-coding genes.},
  article-doi            = {10.1128/genomeA.00111-17},
  article-pii            = {genomeA00111-17},
  electronic-publication = {20170330},
  history                = {2017/04/01 06:01 [medline]},
  issue                  = {13},
  language               = {eng},
  location-id            = {e00111-17},
  nlm-unique-id          = {101595808},
  owner                  = {NLM},
  publication-status     = {epublish},
  revised                = {20201001},
  source                 = {Genome Announc. 2017 Mar 30;5(13):e00111-17. doi: 10.1128/genomeA.00111-17.},
  status                 = {PubMed-not-MEDLINE},
  title-abbreviation     = {Genome Announc},
}

@Article{Vries2017,
  author                 = {de Vries, Ronald P. and Riley, Robert and Wiebenga, Ad and Aguilar-Osorio, Guillermo and Amillis, Sotiris and Uchima, Cristiane Akemi and Anderluh, Gregor and Asadollahi, Mojtaba and Askin, Marion and Barry, Kerrie and Battaglia, Evy and Bayram, Özgür and Benocci, Tiziano and Braus-Stromeyer, Susanna A. and Caldana, Camila and Cánovas, David and Cerqueira, Gustavo C. and Chen, Fusheng and Chen, Wanping and Choi, Cindy and Clum, Alicia and Dos Santos, Renato Augusto Corrêa and Damásio, André Ricardo de Lima and Diallinas, George and Emri, Tamás and Fekete, Erzsébet and Flipphi, Michel and Freyberg, Susanne and Gallo, Antonia and Gournas, Christos and Habgood, Rob and Hainaut, Matthieu and Harispe, María Laura and Henrissat, Bernard and Hildén, Kristiina S. and Hope, Ryan and Hossain, Abeer and Karabika, Eugenia and Karaffa, Levente and Karányi, Zsolt and Kraševec, Nada and Kuo, Alan and Kusch, Harald and LaButti, Kurt and Lagendijk, Ellen L. and Lapidus, Alla and Levasseur, Anthony and Lindquist, Erika and Lipzen, Anna and Logrieco, Antonio F. and MacCabe, Andrew and Mäkelä, Miia R. and Malavazi, Iran and Melin, Petter and Meyer, Vera and Mielnichuk, Natalia and Miskei, Márton and Molnár, Ákos P. and Mulé, Giuseppina and Ngan, Chew Yee and Orejas, Margarita and Orosz, Erzsébet and Ouedraogo, Jean Paul and Overkamp, Karin M. and Park, Hee-Soo and Perrone, Giancarlo and Piumi, Francois and Punt, Peter J. and Ram, Arthur F. J. and Ramón, Ana and Rauscher, Stefan and Record, Eric and Riaño-Pachón, Diego Mauricio and Robert, Vincent and Röhrig, Julian and Ruller, Roberto and Salamov, Asaf and Salih, Nadhira S. and Samson, Rob A. and Sándor, Erzsébet and Sanguinetti, Manuel and Schütze, Tabea and Sepčić, Kristina and Shelest, Ekaterina and Sherlock, Gavin and Sophianopoulou, Vicky and Squina, Fabio M. and Sun, Hui and Susca, Antonia and Todd, Richard B. and Tsang, Adrian and Unkles, Shiela E. and van de Wiele, Nathalie and van Rossen-Uffink, Diana and Oliveira, Juliana Velasco de Castro and Vesth, Tammi C. and Visser, Jaap and Yu, Jae-Hyuk and Zhou, Miaomiao and Andersen, Mikael R. and Archer, David B. and Baker, Scott E. and Benoit, Isabelle and Brakhage, Axel A. and Braus, Gerhard H. and Fischer, Reinhard and Frisvad, Jens C. and Goldman, Gustavo H. and Houbraken, Jos and Oakley, Berl and Pócsi, István and Scazzocchio, Claudio and Seiboth, Bernhard and vanKuyk, Patricia A. and Wortman, Jennifer and Dyer, Paul S. and Grigoriev, Igor V.},
  journal                = {Genome biology},
  title                  = {Comparative genomics reveals high biological diversity and specific adaptations in the industrially and medically important fungal genus Aspergillus.},
  year                   = {2017},
  month                  = {Feb},
  pages                  = {28},
  volume                 = {18},
  abstract               = {BACKGROUND: The fungal genus Aspergillus is of critical importance to humankind. Species include those with industrial applications, important pathogens of humans, animals and crops, a source of potent carcinogenic contaminants of food, and an important genetic model. The genome sequences of eight aspergilli have already been explored to investigate aspects of fungal biology, raising questions about evolution and specialization within this genus. RESULTS: We have generated genome sequences for ten novel, highly diverse Aspergillus species and compared these in detail to sister and more distant genera. Comparative studies of key aspects of fungal biology, including primary and secondary metabolism, stress response, biomass degradation, and signal transduction, revealed both conservation and diversity among the species. Observed genomic differences were validated with experimental studies. This revealed several highlights, such as the potential for sex in asexual species, organic acid production genes being a key feature of black aspergilli, alternative approaches for degrading plant biomass, and indications for the genetic basis of stress response. A genome-wide phylogenetic analysis demonstrated in detail the relationship of the newly genome sequenced species with other aspergilli. CONCLUSIONS: Many aspects of biological differences between fungal species cannot be explained by current knowledge obtained from genome sequences. The comparative genomics and experimental study, presented here, allows for the first time a genus-wide view of the biological diversity of the aspergilli and in many, but not all, cases linked genome differences to phenotype. Insights gained could be exploited for biotechnological and medical applications of fungi.},
  article-doi            = {10.1186/s13059-017-1151-0},
  article-pii            = {1151},
  completed              = {20170707},
  electronic-issn        = {1474-760X},
  electronic-publication = {20170214},
  grantno                = {R01 AI077599/AI/NIAID NIH HHS/United States},
  history                = {2017/07/08 06:00 [medline]},
  issue                  = {1},
  keywords               = {*Adaptation, Biological, Aspergillus/*classification/*genetics/metabolism, *Biodiversity, Biomass, Carbon/metabolism, Computational Biology/methods, Cytochrome P-450 Enzyme System/genetics/metabolism, DNA Methylation, Fungal Proteins/genetics, Gene Expression Regulation, Fungal, Gene Regulatory Networks, *Genome, *Genomics/methods, Humans, Metabolic Networks and Pathways, Molecular Sequence Annotation, Multigene Family, Oxidoreductases/metabolism, Phylogeny, Plants/metabolism/microbiology, Secondary Metabolism/genetics, Signal Transduction, Stress, Physiological/genetics, *Aspergillus, *Comparative genomics, *Fungal biology, *Genome sequencing},
  language               = {eng},
  linking-issn           = {1474-7596},
  location-id            = {28},
  nlm-unique-id          = {100960660},
  owner                  = {NLM},
  print-issn             = {1474-7596},
  publication-status     = {epublish},
  registry-number        = {EC 1.- (Oxidoreductases)},
  revised                = {20210109},
  source                 = {Genome Biol. 2017 Feb 14;18(1):28. doi: 10.1186/s13059-017-1151-0.},
  status                 = {MEDLINE},
  subset                 = {IM},
  termowner              = {NOTNLM},
  title-abbreviation     = {Genome Biol},
}

@Article{PereiraSilva2017,
  author                 = {Pereira Silva, Lilian and Alves de Castro, Patrícia and Dos Reis, Thaila Fernanda and Paziani, Mario Henrique and Von Zeska Kress, Márcia Regina and Riaño-Pachón, Diego Mauricio and Hagiwara, Daisuke and Ries, Laure N. A. and Brown, Neil Andrew and Goldman, Gustavo H.},
  journal                = {Cellular microbiology},
  title                  = {Genome-wide transcriptome analysis of Aspergillus fumigatus exposed to osmotic stress reveals regulators of osmotic and cell wall stresses that are SakA(HOG1) and MpkC dependent.},
  year                   = {2017},
  month                  = {Apr},
  volume                 = {19},
  abstract               = {Invasive aspergillosis is predominantly caused by Aspergillus fumigatus, and adaptations to stresses experienced within the human host are a prerequisite for the survival and virulence strategies of the pathogen. The central signal transduction pathway operating during hyperosmotic stress is the high osmolarity glycerol mitogen-activated protein kinase cascade. A. fumigatus MpkC and SakA, orthologues of the Saccharomyces cerevisiae Hog1p, constitute the primary regulator of the hyperosmotic stress response. We compared A. fumigatus wild-type transcriptional response to osmotic stress with the ΔmpkC, ΔsakA, and ΔmpkC ΔsakA strains. Our results strongly indicate that MpkC and SakA have independent and collaborative functions during the transcriptional response to transient osmotic stress. We have identified and characterized null mutants for four A. fumigatus basic leucine zipper proteins transcription factors. The atfA and atfB have comparable expression levels with the wild-type in ΔmpkC but are repressed in ΔsakA and ΔmpkC ΔsakA post-osmotic stress. The atfC and atfD have reduced expression levels in all mutants post-osmotic stress. The atfA-D null mutants displayed several phenotypes related to osmotic, oxidative, and cell wall stresses. The ΔatfA and ΔatfB were shown to be avirulent and to have attenuated virulence, respectively, in both Galleria mellonella and a neutropenic murine model of invasive pulmonary aspergillosis.},
  address                = {England},
  article-doi            = {10.1111/cmi.12681},
  completed              = {20170724},
  electronic-issn        = {1462-5822},
  electronic-publication = {20161027},
  grantno                = {BB/N011686/1/Biotechnology and Biological Sciences Research Council/United Kingdom},
  history                = {2016/10/06 06:00 [entrez]},
  issue                  = {4},
  keywords               = {Animals, Aspergillosis/*microbiology, Aspergillus fumigatus/*enzymology/genetics, Cell Wall, Female, Fungal Proteins/*genetics/metabolism, Gene Expression Profiling, Gene Expression Regulation, Fungal, Gene Ontology, Genome, Mice, Inbred BALB C, Mitogen-Activated Protein Kinases/*genetics/metabolism, Osmotic Pressure, Signal Transduction, Stress, Physiological, Transcription Factors/physiology, *Transcriptome},
  language               = {eng},
  linking-issn           = {1462-5814},
  location-id            = {10.1111/cmi.12681 [doi]},
  nlm-unique-id          = {100883691},
  owner                  = {NLM},
  publication-status     = {ppublish},
  registry-number        = {EC 2.7.11.24 (Mitogen-Activated Protein Kinases)},
  revised                = {20201209},
  source                 = {Cell Microbiol. 2017 Apr;19(4). doi: 10.1111/cmi.12681. Epub 2016 Oct 27.},
  status                 = {MEDLINE},
  subset                 = {IM},
  title-abbreviation     = {Cell Microbiol},
}

@InProceedings{Winck2016,
  author                 = {Winck, Flavia V. and Riaño-Pachón, Diego Mauricio and Franco, Telma T.},
  booktitle              = {Frontiers in plant science},
  title                  = {Editorial: Advances in Microalgae Biology and Sustainable Applications.},
  year                   = {2016},
  pages                  = {1385},
  volume                 = {7},
  electronic-issn        = {1664-462X},
  linking-issn           = {1664-462X},
  print-issn             = {1664-462X},
  article-doi            = {10.3389/fpls.2016.01385},
  comment                = {The Editorial on the Research Topic Advances in Microalgae Biology and Sustainable Applications},
  electronic-publication = {20160921},
  history                = {2016/10/07 06:01 [medline]},
  keywords               = {bioenergy, biofuels, biomass, biotechnology, carbon dioxide, hydrogen, lipids, nutrients},
  language               = {eng},
  location-id            = {1385},
  nlm-unique-id          = {101568200},
  owner                  = {NLM},
  publication-status     = {epublish},
  revised                = {20201001},
  source                 = {Front Plant Sci. 2016 Sep 21;7:1385. doi: 10.3389/fpls.2016.01385. eCollection 2016.},
  status                 = {PubMed-not-MEDLINE},
  termowner              = {NOTNLM},
  title-abbreviation     = {Front Plant Sci},
}

@Article{AlvesdeCastro2016,
  author                 = {Alves de Castro, Patrícia and Dos Reis, Thaila Fernanda and Dolan, Stephen K. and Oliveira Manfiolli, Adriana and Brown, Neil Andrew and Jones, Gary W. and Doyle, Sean and Riaño-Pachón, Diego Mauricio and Squina, Fábio Márcio and Caldana, Camila and Singh, Ashutosh and Del Poeta, Maurizio and Hagiwara, Daisuke and Silva-Rocha, Rafael and Goldman, Gustavo H.},
  journal                = {Molecular microbiology},
  title                  = {The Aspergillus fumigatus SchA(SCH9) kinase modulates SakA(HOG1) MAP kinase activity and it is essential for virulence.},
  year                   = {2016},
  month                  = {Nov},
  pages                  = {642-671},
  volume                 = {102},
  abstract               = {The serine-threonine kinase TOR, the Target of Rapamycin, is an important regulator of nutrient, energy and stress signaling in eukaryotes. Sch9, a Ser/Thr kinase of AGC family (the cAMP-dependent PKA, cGMP- dependent protein kinase G and phospholipid-dependent protein kinase C family), is a substrate of TOR. Here, we characterized the fungal opportunistic pathogen Aspergillus fumigatus Sch9 homologue (SchA). The schA null mutant was sensitive to rapamycin, high concentrations of calcium, hyperosmotic stress and SchA was involved in iron metabolism. The ΔschA null mutant showed increased phosphorylation of SakA, the A. fumigatus Hog1 homologue. The schA null mutant has increased and decreased trehalose and glycerol accumulation, respectively, suggesting SchA performs different roles for glycerol and trehalose accumulation during osmotic stress. The schA was transcriptionally regulated by osmotic stress and this response was dependent on SakA and MpkC. The double ΔschA ΔsakA and ΔschA ΔmpkC mutants were more sensitive to osmotic stress than the corresponding parental strains. Transcriptomics and proteomics identified direct and indirect targets of SchA post-exposure to hyperosmotic stress. Finally, ΔschA was avirulent in a low dose murine infection model. Our results suggest there is a complex network of interactions amongst the A. fumigatus TOR, SakA and SchA pathways.},
  article-doi            = {10.1111/mmi.13484},
  completed              = {20170731},
  electronic-issn        = {1365-2958},
  electronic-publication = {20161007},
  grantno                = {R01 AI125770/AI/NIAID NIH HHS/United States},
  history                = {2016/08/20 06:00 [entrez]},
  issue                  = {4},
  keywords               = {Animals, Aspergillosis/microbiology, Aspergillus fumigatus/*enzymology/metabolism/*pathogenicity, Female, Fungal Proteins/metabolism, MAP Kinase Signaling System, Mice, Inbred BALB C, Mitogen-Activated Protein Kinases/*metabolism, Osmotic Pressure/physiology, Oxidative Stress/genetics/physiology, Phosphorylation, Protein-Serine-Threonine Kinases/*genetics/metabolism, Signal Transduction, Sirolimus/pharmacology, Spores, Fungal/metabolism, TOR Serine-Threonine Kinases/genetics/metabolism, Virulence},
  language               = {eng},
  linking-issn           = {0950-382X},
  location-id            = {10.1111/mmi.13484 [doi]},
  manuscript-id          = {NIHMS833558},
  nlm-unique-id          = {8712028},
  owner                  = {NLM},
  print-issn             = {0950-382X},
  publication-status     = {ppublish},
  registry-number        = {W36ZG6FT64 (Sirolimus)},
  revised                = {20201209},
  source                 = {Mol Microbiol. 2016 Nov;102(4):642-671. doi: 10.1111/mmi.13484. Epub 2016 Oct 7.},
  status                 = {MEDLINE},
  subset                 = {IM},
  title-abbreviation     = {Mol Microbiol},
}

@Article{Brown2016,
  author                 = {Brown, Neil Andrew and Ries, Laure N. A. and Reis, Thaila F. and Rajendran, Ranjith and Corrêa Dos Santos, Renato Augusto and Ramage, Gordon and Riaño-Pachón, Diego Mauricio and Goldman, Gustavo H.},
  journal                = {Biotechnology for biofuels},
  title                  = {RNAseq reveals hydrophobins that are involved in the adaptation of Aspergillus nidulans to lignocellulose.},
  year                   = {2016},
  pages                  = {145},
  volume                 = {9},
  electronic-issn        = {1754-6834},
  linking-issn           = {1754-6834},
  print-issn             = {1754-6834},
  abstract               = {BACKGROUND: Sugarcane is one of the world's most profitable crops. Waste steam-exploded sugarcane bagasse (SEB) is a cheap, abundant, and renewable lignocellulosic feedstock for the next-generation biofuels. In nature, fungi seldom exist as planktonic cells, similar to those found in the nutrient-rich environment created within an industrial fermenter. Instead, fungi predominantly form biofilms that allow them to thrive in hostile environments. RESULTS: In turn, we adopted an RNA-sequencing approach to interrogate how the model fungus, Aspergillus nidulans, adapts to SEB, revealing the induction of carbon starvation responses and the lignocellulolytic machinery, in addition to morphological adaptations. Genetic analyses showed the importance of hydrophobins for growth on SEB. The major hydrophobin, RodA, was retained within the fungal biofilm on SEB fibres. The StuA transcription factor that regulates fungal morphology was up-regulated during growth on SEB and controlled hydrophobin gene induction. The absence of the RodA or DewC hydrophobins reduced biofilm formation. The loss of a RodA or a functional StuA reduced the retention of the hydrolytic enzymes within the vicinity of the fungus. Hence, hydrophobins promote biofilm formation on SEB, and may enhance lignocellulose utilisation via promoting a compact substrate-enzyme-fungus structure. CONCLUSION: This novel study highlights the importance of hydrophobins to the formation of biofilms and the efficient deconstruction of lignocellulose.},
  article-doi            = {10.1186/s13068-016-0558-2},
  article-pii            = {558},
  completed              = {20160720},
  electronic-publication = {20160719},
  history                = {2016/07/21 06:01 [medline]},
  keywords               = {Biofilm, Fungi, Hydrolytic enzymes, Hydrophobin, Sugarcane bagasse},
  language               = {eng},
  location-id            = {145},
  nlm-unique-id          = {101316935},
  owner                  = {NLM},
  publication-status     = {epublish},
  revised                = {20200930},
  source                 = {Biotechnol Biofuels. 2016 Jul 19;9:145. doi: 10.1186/s13068-016-0558-2. eCollection 2016.},
  status                 = {PubMed-not-MEDLINE},
  termowner              = {NOTNLM},
  title-abbreviation     = {Biotechnol Biofuels},
}

@Article{Winck2016a,
  author                 = {Winck, Flavia V. and Melo, David O. Páez and Riaño-Pachón, Diego Mauricio and Martins, Marina C. M. and Caldana, Camila and Barrios, Andrés F. González},
  journal                = {Frontiers in plant science},
  title                  = {Analysis of Sensitive CO2 Pathways and Genes Related to Carbon Uptake and Accumulation in Chlamydomonas reinhardtii through Genomic Scale Modeling and Experimental Validation.},
  year                   = {2016},
  pages                  = {43},
  volume                 = {7},
  electronic-issn        = {1664-462X},
  linking-issn           = {1664-462X},
  print-issn             = {1664-462X},
  abstract               = {The development of microalgae sustainable applications needs better understanding of microalgae biology. Moreover, how cells coordinate their metabolism toward biomass accumulation is not fully understood. In this present study, flux balance analysis (FBA) was performed to identify sensitive metabolic pathways of Chlamydomonas reinhardtii under varied CO2 inputs. The metabolic network model of Chlamydomonas was updated based on the genome annotation data and sensitivity analysis revealed CO2 sensitive reactions. Biological experiments were performed with cells cultivated at 0.04% (air), 2.5, 5, 8, and 10% CO2 concentration under controlled conditions and cell growth profiles and biomass content were measured. Pigments, lipids, proteins, and starch were further quantified for the reference low (0.04%) and high (10%) CO2 conditions. The expression level of candidate genes of sensitive reactions was measured and validated by quantitative real time PCR. The sensitive analysis revealed mitochondrial compartment as the major affected by changes on the CO2 concentrations and glycolysis/gluconeogenesis, glyoxylate, and dicarboxylate metabolism among the affected metabolic pathways. Genes coding for glycerate kinase (GLYK), glycine cleavage system, H-protein (GCSH), NAD-dependent malate dehydrogenase (MDH3), low-CO2 inducible protein A (LCIA), carbonic anhydrase 5 (CAH5), E1 component, alpha subunit (PDC3), dual function alcohol dehydrogenase/acetaldehyde dehydrogenase (ADH1), and phosphoglucomutase (GPM2), were defined, among other genes, as sensitive nodes in the metabolic network simulations. These genes were experimentally responsive to the changes in the carbon fluxes in the system. We performed metabolomics analysis using mass spectrometry validating the modulation of carbon dioxide responsive pathways and metabolites. The changes on CO2 levels mostly affected the metabolism of amino acids found in the photorespiration pathway. Our updated metabolic network was compared to previous model and it showed more consistent results once considering the experimental data. Possible roles of the sensitive pathways in the biomass metabolism are discussed.},
  article-doi            = {10.3389/fpls.2016.00043},
  completed              = {20160223},
  electronic-publication = {20160209},
  history                = {2016/02/24 06:01 [medline]},
  keywords               = {bioenergy, biomass, biotechnology, carbon uptake, chlamydomonas, flux balance analysis, microalgae, systems biology},
  language               = {eng},
  location-id            = {43},
  nlm-unique-id          = {101568200},
  owner                  = {NLM},
  publication-status     = {epublish},
  revised                = {20200930},
  source                 = {Front Plant Sci. 2016 Feb 9;7:43. doi: 10.3389/fpls.2016.00043. eCollection 2016.},
  status                 = {PubMed-not-MEDLINE},
  termowner              = {NOTNLM},
  title-abbreviation     = {Front Plant Sci},
}

@Article{Mattiello2015,
  author                 = {Mattiello, Lucia and Riaño-Pachón, Diego Mauricio and Martins, Marina Camara Mattos and da Cruz, Larissa Prado and Bassi, Denis and Marchiori, Paulo Eduardo Ribeiro and Ribeiro, Rafael Vasconcelos and Labate, Mônica T. Veneziano and Labate, Carlos Alberto and Menossi, Marcelo},
  journal                = {BMC plant biology},
  title                  = {Physiological and transcriptional analyses of developmental stages along sugarcane leaf.},
  year                   = {2015},
  month                  = {Dec},
  pages                  = {300},
  volume                 = {15},
  electronic-issn        = {1471-2229},
  linking-issn           = {1471-2229},
  abstract               = {BACKGROUND: Sugarcane is one of the major crops worldwide. It is cultivated in over 100 countries on 22 million ha. The complex genetic architecture and the lack of a complete genomic sequence in sugarcane hamper the adoption of molecular approaches to study its physiology and to develop new varieties. Investments on the development of new sugarcane varieties have been made to maximize sucrose yield, a trait dependent on photosynthetic capacity. However, detailed studies on sugarcane leaves are scarce. In this work, we report the first molecular and physiological characterization of events taking place along a leaf developmental gradient in sugarcane. RESULTS: Photosynthetic response to CO2 indicated divergence in photosynthetic capacity based on PEPcase activity, corroborated by activity quantification (both in vivo and in vitro) and distinct levels of carbon discrimination on different segments along leaf length. Additionally, leaf segments had contrasting amount of chlorophyll, nitrogen and sugars. RNA-Seq data indicated a plethora of biochemical pathways differentially expressed along the leaf. Some transcription factors families were enriched on each segment and their putative functions corroborate with the distinct developmental stages. Several genes with higher expression in the middle segment, the one with the highest photosynthetic rates, were identified and their role in sugarcane productivity is discussed. Interestingly, sugarcane leaf segments had a different transcriptional behavior compared to previously published data from maize. CONCLUSION: This is the first report of leaf developmental analysis in sugarcane. Our data on sugarcane is another source of information for further studies aiming to understand and/or improve C4 photosynthesis. The segments used in this work were distinct in their physiological status allowing deeper molecular analysis. Although limited in some aspects, the comparison to maize indicates that all data acquired on one C4 species cannot always be easily extrapolated to other species. However, our data indicates that some transcriptional factors were segment-specific and the sugarcane leaf undergoes through the process of suberizarion, photosynthesis establishment and senescence.},
  article-doi            = {10.1186/s12870-015-0694-z},
  article-pii            = {694},
  completed              = {20160701},
  electronic-publication = {20151229},
  history                = {2016/07/02 06:00 [medline]},
  keywords               = {*Gene Expression Regulation, Plant, Molecular Sequence Data, Plant Leaves/genetics/growth & development, Plant Proteins/*genetics/metabolism, Saccharum/*genetics/*growth & development, Sequence Analysis, DNA},
  language               = {eng},
  location-id            = {300},
  nlm-unique-id          = {100967807},
  owner                  = {NLM},
  publication-status     = {epublish},
  registry-number        = {0 (Plant Proteins)},
  revised                = {20190109},
  second-id              = {SRA/SRR1979669},
  source                 = {BMC Plant Biol. 2015 Dec 29;15:300. doi: 10.1186/s12870-015-0694-z.},
  status                 = {MEDLINE},
  subset                 = {IM},
  title-abbreviation     = {BMC Plant Biol},
}

@Article{DosSantos2015,
  author                 = {Dos Santos, Renato Augusto Corrêa and Berretta, Andresa Aparecida and Barud, Hernane da Silva and Ribeiro, Sidney José Lima and González-García, Laura Natalia and Zucchi, Tiago Domingues and Goldman, Gustavo H. and Riaño-Pachón, Diego Mauricio},
  journal                = {Genome announcements},
  title                  = {Draft Genome Sequence of Komagataeibacter intermedius Strain AF2, a Producer of Cellulose, Isolated from Kombucha Tea.},
  year                   = {2015},
  month                  = {Dec},
  volume                 = {3},
  electronic-issn        = {2169-8287},
  print-issn             = {2169-8287},
  abstract               = {Here, we present the draft genome sequence of Komagataeibacter intermedius strain AF2, which was isolated from Kombucha tea and is capable of producing cellulose, although at lower levels compared to another bacterium from the same environment, K. rhaeticus strain AF1.},
  article-doi            = {10.1128/genomeA.01404-15},
  article-pii            = {genomeA01404-15},
  completed              = {20151204},
  electronic-publication = {20151203},
  history                = {2015/12/05 06:01 [medline]},
  issue                  = {6},
  language               = {eng},
  location-id            = {e01404-15},
  nlm-unique-id          = {101595808},
  owner                  = {NLM},
  publication-status     = {epublish},
  revised                = {20200929},
  source                 = {Genome Announc. 2015 Dec 3;3(6):e01404-15. doi: 10.1128/genomeA.01404-15.},
  status                 = {PubMed-not-MEDLINE},
  title-abbreviation     = {Genome Announc},
}

@Article{Winck2015,
  author                 = {Winck, Flavia V. and Prado Ribeiro, Ana Carolina and Ramos Domingues, Romênia and Ling, Liu Yi and Riaño-Pachón, Diego Mauricio and Rivera, César and Brandão, Thaís Bianca and Gouvea, Adriele Ferreira and Santos-Silva, Alan Roger and Coletta, Ricardo D. and Paes Leme, Adriana F.},
  journal                = {Scientific reports},
  title                  = {Insights into immune responses in oral cancer through proteomic analysis of saliva and salivary extracellular vesicles.},
  year                   = {2015},
  month                  = {Nov},
  pages                  = {16305},
  volume                 = {5},
  abstract               = {The development and progression of oral cavity squamous cell carcinoma (OSCC) involves complex cellular mechanisms that contribute to the low five-year survival rate of approximately 20% among diagnosed patients. However, the biological processes essential to tumor progression are not completely understood. Therefore, detecting alterations in the salivary proteome may assist in elucidating the cellular mechanisms modulated in OSCC and improve the clinical prognosis of the disease. The proteome of whole saliva and salivary extracellular vesicles (EVs) from patients with OSCC and healthy individuals were analyzed by LC-MS/MS and label-free protein quantification. Proteome data analysis was performed using statistical, machine learning and feature selection methods with additional functional annotation. Biological processes related to immune responses, peptidase inhibitor activity, iron coordination and protease binding were overrepresented in the group of differentially expressed proteins. Proteins related to the inflammatory system, transport of metals and cellular growth and proliferation were identified in the proteome of salivary EVs. The proteomics data were robust and could classify OSCC with 90% accuracy. The saliva proteome analysis revealed that immune processes are related to the presence of OSCC and indicate that proteomics data can contribute to determining OSCC prognosis.},
  article-doi            = {10.1038/srep16305},
  article-pii            = {srep16305},
  completed              = {20160923},
  electronic-issn        = {2045-2322},
  electronic-publication = {20151105},
  history                = {2016/09/24 06:00 [medline]},
  keywords               = {Adult, Aged, 80 and over, Biomarkers, Tumor/immunology/metabolism, Chromatography, Liquid/methods, Extracellular Vesicles/immunology/*metabolism, Female, Humans, Male, Middle Aged, Mouth Neoplasms/*immunology/*metabolism, Prognosis, Proteome/*immunology/*metabolism, Proteomics/methods, Saliva/immunology/*metabolism, Tandem Mass Spectrometry/methods},
  language               = {eng},
  linking-issn           = {2045-2322},
  location-id            = {16305},
  nlm-unique-id          = {101563288},
  owner                  = {NLM},
  publication-status     = {epublish},
  registry-number        = {0 (Proteome)},
  revised                = {20181113},
  source                 = {Sci Rep. 2015 Nov 5;5:16305. doi: 10.1038/srep16305.},
  status                 = {MEDLINE},
  subset                 = {IM},
  title-abbreviation     = {Sci Rep},
}

@Article{Marine2015,
  author                 = {Mariné, Marçal and Brown, Neil Andrew and Riaño-Pachón, Diego Mauricio and Goldman, Gustavo Henrique},
  journal                = {PLoS pathogens},
  title                  = {On and Under the Skin: Emerging Basidiomycetous Yeast Infections Caused by Trichosporon Species.},
  year                   = {2015},
  month                  = {Jul},
  pages                  = {e1004982},
  volume                 = {11},
  electronic-issn        = {1553-7374},
  linking-issn           = {1553-7366},
  print-issn             = {1553-7366},
  article-doi            = {10.1371/journal.ppat.1004982},
  article-pii            = {PPATHOGENS-D-15-00581},
  completed              = {20160405},
  electronic-publication = {20150730},
  history                = {2016/04/06 06:00 [medline]},
  issue                  = {7},
  keywords               = {Animals, DNA, Ribosomal/*genetics, Humans, Mycological Typing Techniques/methods, Piedra/diagnosis/microbiology/*therapy, Skin/*microbiology, Trichosporon/classification/*pathogenicity, Trichosporonosis/diagnosis/*microbiology/*therapy, Yeasts},
  language               = {eng},
  location-id            = {e1004982},
  nlm-unique-id          = {101238921},
  owner                  = {NLM},
  publication-status     = {epublish},
  registry-number        = {0 (DNA, Ribosomal)},
  revised                = {20190202},
  source                 = {PLoS Pathog. 2015 Jul 30;11(7):e1004982. doi: 10.1371/journal.ppat.1004982. eCollection 2015 Jul.},
  status                 = {MEDLINE},
  subset                 = {IM},
  title-abbreviation     = {PLoS Pathog},
}

@Article{RosasMorales2015,
  author                 = {Rosas-Morales, Juan Pablo and Perez-Mancilla, Ximena and López-Kleine, Liliana and Montoya Castaño, Dolly and Riaño-Pachón, Diego Mauricio},
  journal                = {Genome announcements},
  title                  = {Draft genome sequences of clostridium strains native to Colombia with the potential to produce solvents.},
  year                   = {2015},
  month                  = {May},
  volume                 = {3},
  electronic-issn        = {2169-8287},
  print-issn             = {2169-8287},
  abstract               = {Genomes from four Clostridium sp. strains considered to be mesophilic anaerobic bacteria, isolated from crop soil in Colombia, with a strong potential to produce alcohols like 1,3-propanediol, were analyzed. We present the draft genome of these strains, which will be useful for developing genetic engineering strategies.},
  article-doi            = {10.1128/genomeA.00486-15},
  article-pii            = {genomeA00486-15},
  completed              = {20150522},
  electronic-publication = {20150521},
  history                = {2015/05/23 06:01 [medline]},
  issue                  = {3},
  language               = {eng},
  location-id            = {e00486-15},
  nlm-unique-id          = {101595808},
  owner                  = {NLM},
  publication-status     = {epublish},
  revised                = {20200930},
  source                 = {Genome Announc. 2015 May 21;3(3):e00486-15. doi: 10.1128/genomeA.00486-15.},
  status                 = {PubMed-not-MEDLINE},
  title-abbreviation     = {Genome Announc},
}

@Article{Mandelli2015,
  author                 = {Mandelli, Fernanda and Oliveira Ramires, Brenda and Couger, Matthew Brian and Paixão, Douglas A. A. and Camilo, Cesar M. and Polikarpov, Igor and Prade, Rolf and Riaño-Pachón, Diego Mauricio and Squina, Fabio M.},
  journal                = {Genome announcements},
  title                  = {Draft Genome Sequence of the Thermophile Thermus filiformis ATCC 43280, Producer of Carotenoid-(Di)glucoside-Branched Fatty Acid (Di)esters and Source of Hyperthermostable Enzymes of Biotechnological Interest.},
  year                   = {2015},
  month                  = {May},
  volume                 = {3},
  electronic-issn        = {2169-8287},
  print-issn             = {2169-8287},
  abstract               = {Here, we present the draft genome sequence of Thermus filiformis strain ATCC 43280, a thermophile bacterium capable of producing glycosylated carotenoids acylated with branched fatty acids and enzymes of biotechnological potential.},
  article-doi            = {10.1128/genomeA.00475-15},
  article-pii            = {genomeA00475-15},
  completed              = {20150515},
  electronic-publication = {20150514},
  history                = {2015/05/16 06:01 [medline]},
  issue                  = {3},
  language               = {eng},
  location-id            = {e00475-15},
  nlm-unique-id          = {101595808},
  owner                  = {NLM},
  publication-status     = {epublish},
  revised                = {20200930},
  source                 = {Genome Announc. 2015 May 14;3(3):e00475-15. doi: 10.1128/genomeA.00475-15.},
  status                 = {PubMed-not-MEDLINE},
  title-abbreviation     = {Genome Announc},
}

@Article{Cristancho2014,
  author                 = {Cristancho, Marco A. and Botero-Rozo, David Octavio and Giraldo, William and Tabima, Javier and Riaño-Pachón, Diego Mauricio and Escobar, Carolina and Rozo, Yomara and Rivera, Luis F. and Durán, Andrés and Restrepo, Silvia and Eilam, Tamar and Anikster, Yehoshua and Gaitán, Alvaro L.},
  journal                = {Frontiers in plant science},
  title                  = {Annotation of a hybrid partial genome of the coffee rust (Hemileia vastatrix) contributes to the gene repertoire catalog of the Pucciniales.},
  year                   = {2014},
  pages                  = {594},
  volume                 = {5},
  electronic-issn        = {1664-462X},
  linking-issn           = {1664-462X},
  print-issn             = {1664-462X},
  abstract               = {Coffee leaf rust caused by the fungus Hemileia vastatrix is the most damaging disease to coffee worldwide. The pathogen has recently appeared in multiple outbreaks in coffee producing countries resulting in significant yield losses and increases in costs related to its control. New races/isolates are constantly emerging as evidenced by the presence of the fungus in plants that were previously resistant. Genomic studies are opening new avenues for the study of the evolution of pathogens, the detailed description of plant-pathogen interactions and the development of molecular techniques for the identification of individual isolates. For this purpose we sequenced 8 different H. vastatrix isolates using NGS technologies and gathered partial genome assemblies due to the large repetitive content in the coffee rust hybrid genome; 74.4% of the assembled contigs harbor repetitive sequences. A hybrid assembly of 333 Mb was built based on the 8 isolates; this assembly was used for subsequent analyses. Analysis of the conserved gene space showed that the hybrid H. vastatrix genome, though highly fragmented, had a satisfactory level of completion with 91.94% of core protein-coding orthologous genes present. RNA-Seq from urediniospores was used to guide the de novo annotation of the H. vastatrix gene complement. In total, 14,445 genes organized in 3921 families were uncovered; a considerable proportion of the predicted proteins (73.8%) were homologous to other Pucciniales species genomes. Several gene families related to the fungal lifestyle were identified, particularly 483 predicted secreted proteins that represent candidate effector genes and will provide interesting hints to decipher virulence in the coffee rust fungus. The genome sequence of Hva will serve as a template to understand the molecular mechanisms used by this fungus to attack the coffee plant, to study the diversity of this species and for the development of molecular markers to distinguish races/isolates.},
  article-doi            = {10.3389/fpls.2014.00594},
  completed              = {20141117},
  electronic-publication = {20141031},
  history                = {2014/11/18 06:01 [medline]},
  keywords               = {RNA-seq, coffee, coffee rust, genetic variants, genome, plant pathogens diversity},
  language               = {eng},
  location-id            = {594},
  nlm-unique-id          = {101568200},
  owner                  = {NLM},
  publication-status     = {epublish},
  revised                = {20200930},
  source                 = {Front Plant Sci. 2014 Oct 31;5:594. doi: 10.3389/fpls.2014.00594. eCollection 2014.},
  status                 = {PubMed-not-MEDLINE},
  termowner              = {NOTNLM},
  title-abbreviation     = {Front Plant Sci},
}

@Article{BuitragoFlorez2014,
  author                 = {Buitrago-Flórez, Francisco Javier and Restrepo, Silvia and Riaño-Pachón, Diego Mauricio},
  journal                = {PloS one},
  title                  = {Identification of transcription factor genes and their correlation with the high diversity of stramenopiles.},
  year                   = {2014},
  pages                  = {e111841},
  volume                 = {9},
  electronic-issn        = {1932-6203},
  linking-issn           = {1932-6203},
  abstract               = {The biological diversity among Stramenopiles is striking; they range from large multicellular seaweeds to tiny unicellular species, they embrace many ecologically important autothrophic (e.g., diatoms, brown algae), and heterotrophic (e.g., oomycetes) groups. Transcription factors (TFs) and other transcription regulators (TRs) regulate spatial and temporal gene expression. A plethora of transcriptional regulatory proteins have been identified and classified into families on the basis of sequence similarity. The purpose of this work is to identify the TF and TR complement in diverse species belonging to Stramenopiles in order to understand how these regulators may contribute to their observed diversity. We identified and classified 63 TF and TR families in 11 species of Stramenopiles. In some species we found gene families with high relative importance. Taking into account the 63 TF and TR families identified, 28 TF and TR families were established to be positively correlated with specific traits like number of predicted proteins, number of flagella and number of cell types during the life cycle. Additionally, we found gains and losses in TF and TR families specific to some species and clades, as well as, two families with high abundance specific to the autotrophic species and three families with high abundance specific to the heterotropic species. For the first time, there is a systematic search of TF and TR families in Stramenopiles. The attempts to uncover relationships between these families and the complexity of this group may be of great impact, considering that there are several important pathogens of plants and animals, as well as, important species involved in carbon cycling. Specific TF and TR families identified in this work appear to be correlated with particular traits in the Stramenopiles group and may be correlated with the high complexity and diversity in Stramenopiles.},
  article-doi            = {10.1371/journal.pone.0111841},
  article-pii            = {PONE-D-14-20048},
  completed              = {20150714},
  electronic-publication = {20141106},
  history                = {2015/07/15 06:00 [medline]},
  issue                  = {11},
  keywords               = {Animals, Biodiversity, Evolution, Molecular, Gene Expression Regulation, Genome, Multigene Family, Phylogeny, Stramenopiles/*classification/*genetics, Transcription Factors/*genetics},
  language               = {eng},
  location-id            = {e111841},
  nlm-unique-id          = {101285081},
  owner                  = {NLM},
  publication-status     = {epublish},
  registry-number        = {0 (Transcription Factors)},
  revised                = {20181113},
  source                 = {PLoS One. 2014 Nov 6;9(11):e111841. doi: 10.1371/journal.pone.0111841. eCollection 2014.},
  status                 = {MEDLINE},
  subset                 = {IM},
  title-abbreviation     = {PLoS One},
}

@Article{DosSantos2014,
  author                 = {Dos Santos, Renato Augusto Corrêa and Berretta, Andresa A. and Barud, Hernane da Silva and Ribeiro, Sidney José Lima and González-García, Laura Natalia and Zucchi, Tiago Domingues and Goldman, Gustavo H. and Riaño-Pachón, Diego Mauricio},
  journal                = {Genome announcements},
  title                  = {Draft Genome Sequence of Komagataeibacter rhaeticus Strain AF1, a High Producer of Cellulose, Isolated from Kombucha Tea.},
  year                   = {2014},
  month                  = {Jul},
  volume                 = {2},
  electronic-issn        = {2169-8287},
  print-issn             = {2169-8287},
  abstract               = {Here, we present the draft genome sequence of Komagatabaeicter rhaeticus strain AF1, which was isolated from Kombucha tea and is capable of producing high levels of cellulose.},
  article-doi            = {10.1128/genomeA.00731-14},
  article-pii            = {genomeA00731-14},
  completed              = {20140725},
  electronic-publication = {20140724},
  history                = {2014/07/26 06:01 [medline]},
  issue                  = {4},
  language               = {eng},
  location-id            = {e00731-14},
  nlm-unique-id          = {101595808},
  owner                  = {NLM},
  publication-status     = {epublish},
  revised                = {20211021},
  source                 = {Genome Announc. 2014 Jul 24;2(4):e00731-14. doi: 10.1128/genomeA.00731-14.},
  status                 = {PubMed-not-MEDLINE},
  title-abbreviation     = {Genome Announc},
}

@Article{Oliveira2014,
  author                 = {Oliveira, Juliana Velasco de Castro and Borges, Thuanny A. and Corrêa Dos Santos, Renato Augusto and Freitas, Larissa F. D. and Rosa, Carlos Augusto and Goldman, Gustavo Henrique and Riaño-Pachón, Diego Mauricio},
  journal                = {International journal of systematic and evolutionary microbiology},
  title                  = {Pseudozyma brasiliensis sp. nov., a xylanolytic, ustilaginomycetous yeast species isolated from an insect pest of sugarcane roots.},
  year                   = {2014},
  month                  = {Jun},
  pages                  = {2159-2168},
  volume                 = {64},
  abstract               = {A novel ustilaginomycetous yeast isolated from the intestinal tract of an insect pest of sugarcane roots in Ribeirão Preto, São Paulo State, Brazil, represents a novel species of the genus Pseudozyma based on molecular analyses of the D1/D2 rDNA large subunit and the internal transcribed spacer (ITS1+ITS2) regions. The name Pseudozyma brasiliensis sp. nov. is proposed for this species, with GHG001(T) ( = CBS 13268(T) = UFMG-CM-Y307(T)) as the type strain. P. brasiliensis sp. nov. is a sister species of Pseudozyma vetiver, originally isolated from leaves of vetiver grass and sugarcane in Thailand. P. brasiliensis sp. nov. is able to grow well with xylan as the sole carbon source and produces high levels of an endo-1,4-xylanase that has a higher specific activity in comparison with other eukaryotic xylanases. This enzyme has a variety of industrial applications, indicating the great biotechnological potential of P. brasiliensis.},
  address                = {England},
  article-doi            = {10.1099/ijs.0.060103-0},
  completed              = {20140728},
  electronic-issn        = {1466-5034},
  electronic-publication = {20140328},
  history                = {2014/07/30 06:00 [medline]},
  issue                  = {Pt 6},
  keywords               = {Animals, Brazil, DNA, Fungal/genetics, Ribosomal Spacer/genetics, Endo-1, 4-beta Xylanases/metabolism, Insecta/*microbiology, Intestines/microbiology, Molecular Sequence Data, Mycological Typing Techniques, *Phylogeny, Plant Roots, *Saccharum, Sequence Analysis, Ustilaginales/*classification/genetics/isolation & purification},
  language               = {eng},
  linking-issn           = {1466-5026},
  location-id            = {10.1099/ijs.0.060103-0 [doi]},
  nlm-unique-id          = {100899600},
  owner                  = {NLM},
  publication-status     = {ppublish},
  registry-number        = {EC 3.2.1.8 (Endo-1,4-beta Xylanases)},
  revised                = {20200516},
  second-id              = {GENBANK/KF737866},
  source                 = {Int J Syst Evol Microbiol. 2014 Jun;64(Pt 6):2159-2168. doi: 10.1099/ijs.0.060103-0. Epub 2014 Mar 28.},
  status                 = {MEDLINE},
  subset                 = {IM},
  title-abbreviation     = {Int J Syst Evol Microbiol},
}

@Article{Omidbakhshfard2014,
  author                 = {Omidbakhshfard, Mohammad Amin and Winck, Flavia Vischi and Arvidsson, Samuel and Riaño-Pachón, Diego Mauricio and Mueller-Roeber, Bernd},
  journal                = {Journal of integrative plant biology},
  title                  = {A step-by-step protocol for formaldehyde-assisted isolation of regulatory elements from Arabidopsis thaliana.},
  year                   = {2014},
  month                  = {Jun},
  pages                  = {527-38},
  volume                 = {56},
  abstract               = {The control of gene expression by transcriptional regulators and other types of functionally relevant DNA transactions such as chromatin remodeling and replication underlie a vast spectrum of biological processes in all organisms. DNA transactions require the controlled interaction of proteins with DNA sequence motifs which are often located in nucleosome-depleted regions (NDRs) of the chromatin. Formaldehyde-assisted isolation of regulatory elements (FAIRE) has been established as an easy-to-implement method for the isolation of NDRs from a number of eukaryotic organisms, and it has been successfully employed for the discovery of new regulatory segments in genomic DNA from, for example, yeast, Drosophila, and humans. Until today, however, FAIRE has only rarely been employed in plant research and currently no detailed FAIRE protocol for plants has been published. Here, we provide a step-by-step FAIRE protocol for NDR discovery in Arabidopsis thaliana. We demonstrate that NDRs isolated from plant chromatin are readily amenable to quantitative polymerase chain reaction and next-generation sequencing. Only minor modification of the FAIRE protocol will be needed to adapt it to other plants, thus facilitating the global inventory of regulatory regions across species.},
  address                = {China (Republic : 1949- )},
  article-doi            = {10.1111/jipb.12151},
  completed              = {20150128},
  electronic-issn        = {1744-7909},
  electronic-publication = {20140316},
  history                = {2015/01/30 06:00 [medline]},
  issue                  = {6},
  keywords               = {Arabidopsis/drug effects/*genetics, Chromosomes, Plant/genetics, DNA, Plant/genetics/*isolation & purification, Formaldehyde/*pharmacology, Genes, Essential, Genome, High-Throughput Nucleotide Sequencing, Molecular Biology/*methods, Polymerase Chain Reaction, Regulatory Sequences, Nucleic Acid/*genetics, Sonication, Arabidopsis thaliana, FAIRE-qPCR, FAIRE-seq, chromatin, cis-regulatory elements, epigenomics, gene expression, gene regulatory network, transcription factor},
  language               = {eng},
  linking-issn           = {1672-9072},
  location-id            = {10.1111/jipb.12151 [doi]},
  nlm-unique-id          = {101250502},
  owner                  = {NLM},
  publication-status     = {ppublish},
  registry-number        = {1HG84L3525 (Formaldehyde)},
  revised                = {20140606},
  source                 = {J Integr Plant Biol. 2014 Jun;56(6):527-38. doi: 10.1111/jipb.12151. Epub 2014 Mar 16.},
  status                 = {MEDLINE},
  subset                 = {IM},
  termowner              = {NOTNLM},
  title-abbreviation     = {J Integr Plant Biol},
}

@Article{Oliveira2013,
  author                 = {Oliveira, Juliana Velasco de Castro and Dos Santos, Renato Augusto Corrêa and Borges, Thuanny A. and Riaño-Pachón, Diego Mauricio and Goldman, Gustavo Henrique},
  journal                = {Genome announcements},
  title                  = {Draft Genome Sequence of Pseudozyma brasiliensis sp. nov. Strain GHG001, a High Producer of Endo-1,4-Xylanase Isolated from an Insect Pest of Sugarcane.},
  year                   = {2013},
  month                  = {Dec},
  volume                 = {1},
  electronic-issn        = {2169-8287},
  print-issn             = {2169-8287},
  abstract               = {Here, we present the nuclear and mitochondrial genome sequences of Pseudozyma brasiliensis sp. nov. strain GHG001. P. brasiliensis sp. nov. is the closest relative of Pseudozyma vetiver. P. brasiliensis sp. nov. is capable of growing on xylose or xylan as a sole carbon source and has great biotechnological potential.},
  article-doi            = {10.1128/genomeA.00920-13},
  article-pii            = {genomeA00920-13},
  completed              = {20131220},
  electronic-publication = {20131219},
  history                = {2013/12/21 06:01 [medline]},
  issue                  = {6},
  language               = {eng},
  location-id            = {e00920-13},
  nlm-unique-id          = {101595808},
  owner                  = {NLM},
  publication-status     = {epublish},
  revised                = {20211021},
  source                 = {Genome Announc. 2013 Dec 19;1(6):e00920-13. doi: 10.1128/genomeA.00920-13.},
  status                 = {PubMed-not-MEDLINE},
  title-abbreviation     = {Genome Announc},
}

@Article{Winck2013,
  author                 = {Winck, Flavia Vischi and Arvidsson, Samuel and Riaño-Pachón, Diego Mauricio and Hempel, Sabrina and Koseska, Aneta and Nikoloski, Zoran and Urbina Gomez, David Alejandro and Rupprecht, Jens and Mueller-Roeber, Bernd},
  journal                = {PloS one},
  title                  = {Genome-wide identification of regulatory elements and reconstruction of gene regulatory networks of the green alga Chlamydomonas reinhardtii under carbon deprivation.},
  year                   = {2013},
  pages                  = {e79909},
  volume                 = {8},
  electronic-issn        = {1932-6203},
  linking-issn           = {1932-6203},
  abstract               = {The unicellular green alga Chlamydomonas reinhardtii is a long-established model organism for studies on photosynthesis and carbon metabolism-related physiology. Under conditions of air-level carbon dioxide concentration [CO2], a carbon concentrating mechanism (CCM) is induced to facilitate cellular carbon uptake. CCM increases the availability of carbon dioxide at the site of cellular carbon fixation. To improve our understanding of the transcriptional control of the CCM, we employed FAIRE-seq (formaldehyde-assisted Isolation of Regulatory Elements, followed by deep sequencing) to determine nucleosome-depleted chromatin regions of algal cells subjected to carbon deprivation. Our FAIRE data recapitulated the positions of known regulatory elements in the promoter of the periplasmic carbonic anhydrase (Cah1) gene, which is upregulated during CCM induction, and revealed new candidate regulatory elements at a genome-wide scale. In addition, time series expression patterns of 130 transcription factor (TF) and transcription regulator (TR) genes were obtained for cells cultured under photoautotrophic condition and subjected to a shift from high to low [CO2]. Groups of co-expressed genes were identified and a putative directed gene-regulatory network underlying the CCM was reconstructed from the gene expression data using the recently developed IOTA (inner composition alignment) method. Among the candidate regulatory genes, two members of the MYB-related TF family, Lcr1 (Low-CO 2 response regulator 1) and Lcr2 (Low-CO2 response regulator 2), may play an important role in down-regulating the expression of a particular set of TF and TR genes in response to low [CO2]. The results obtained provide new insights into the transcriptional control of the CCM and revealed more than 60 new candidate regulatory genes. Deep sequencing of nucleosome-depleted genomic regions indicated the presence of new, previously unknown regulatory elements in the C. reinhardtii genome. Our work can serve as a basis for future functional studies of transcriptional regulator genes and genomic regulatory elements in Chlamydomonas.},
  article-doi            = {10.1371/journal.pone.0079909},
  article-pii            = {PONE-D-12-35326},
  comment                = {PLoS One. 2014;9(1). doi:10.1371/annotation/63d1c5f9-82c8-406b-b60e-b7d9ecba9408. Vischi Winck, Flavia [corrected to Winck, Flavia Vischi]},
  completed              = {20140620},
  electronic-publication = {20131101},
  history                = {2014/06/21 06:00 [medline]},
  issue                  = {11},
  keywords               = {Carbon/deficiency/*metabolism, Carbonic Anhydrases/genetics/metabolism, Chlamydomonas reinhardtii/genetics/*metabolism, Gene Regulatory Networks/genetics/physiology, Transcription Factors/genetics/metabolism},
  language               = {eng},
  location-id            = {e79909},
  nlm-unique-id          = {101285081},
  owner                  = {NLM},
  publication-status     = {epublish},
  registry-number        = {EC 4.2.1.1 (Carbonic Anhydrases)},
  revised                = {20211021},
  source                 = {PLoS One. 2013 Nov 1;8(11):e79909. doi: 10.1371/journal.pone.0079909. eCollection 2013.},
  status                 = {MEDLINE},
  subset                 = {IM},
  title-abbreviation     = {PLoS One},
}

@Article{LopezKleine2013,
  author                 = {López-Kleine, Liliana and Pinzón, Andrés and Chaves, Diego and Restrepo, Silvia and Riaño-Pachón, Diego Mauricio},
  journal                = {Genomics},
  title                  = {Chromosome 10 in the tomato plant carries clusters of genes responsible for field resistance/defence to Phytophthora infestans.},
  year                   = {2013},
  month                  = {Apr},
  pages                  = {249-55},
  volume                 = {101},
  electronic-issn        = {1089-8646},
  linking-issn           = {0888-7543},
  abstract               = {The main objective of the present study was to reanalyse tomato expression data that was previously submitted to the Tomato Expression Database to dissect the resistance/defence genomic and metabolic responses of tomato to Phytophthora infestans under field conditions. Overrepresented gene sets belonging to chromosome 10 were identified using the Gene Set Enrichment Analysis, and we found that these genes tend to be located towards the end of the chromosome 10. An analysis of syntenic regions between Arabidopsis thaliana chromosomes and the tomato chromosome 10 allowed us to identify conserved regions in the two genomes. In addition to allowing for the identification of tomato candidate genes participating in resistance/defence in the field, this approach allowed us to investigate the relationships of the candidate genes with chromosomal position and participation in metabolic functions, thus offering more insight into the phenomena occurring during the infection process.},
  address                = {United States},
  article-doi            = {10.1016/j.ygeno.2013.02.001},
  article-pii            = {S0888-7543(13)00017-7},
  completed              = {20130905},
  electronic-publication = {20130209},
  history                = {2013/09/06 06:00 [medline]},
  issue                  = {4},
  keywords               = {Arabidopsis/genetics, Chromosomes, Plant/*genetics, Conserved Sequence, Databases, Genetic, Disease Resistance/*genetics, *Genes, Plant, Lycopersicon esculentum/*genetics/metabolism/microbiology, Multigene Family, *Phytophthora infestans, Synteny},
  language               = {eng},
  location-id            = {10.1016/j.ygeno.2013.02.001 [doi]},
  nlm-unique-id          = {8800135},
  owner                  = {NLM},
  publication-status     = {ppublish},
  revised                = {20130325},
  source                 = {Genomics. 2013 Apr;101(4):249-55. doi: 10.1016/j.ygeno.2013.02.001. Epub 2013 Feb 9.},
  status                 = {MEDLINE},
  subset                 = {IM},
  title-abbreviation     = {Genomics},
}

@Article{Dreyer2012,
  author                 = {Dreyer, Ingo and Gomez-Porras, Judith Lucia and Riaño-Pachón, Diego Mauricio and Hedrich, Rainer and Geiger, Dietmar},
  journal                = {Frontiers in plant science},
  title                  = {Molecular Evolution of Slow and Quick Anion Channels (SLACs and QUACs/ALMTs).},
  year                   = {2012},
  pages                  = {263},
  volume                 = {3},
  electronic-issn        = {1664-462X},
  linking-issn           = {1664-462X},
  abstract               = {Electrophysiological analyses conducted about 25 years ago detected two types of anion channels in the plasma membrane of guard cells. One type of channel responds slowly to changes in membrane voltage while the other responds quickly. Consequently, they were named SLAC, for SLow Anion Channel, and QUAC, for QUick Anion Channel. Recently, genes SLAC1 and QUAC1/ALMT12, underlying the two different anion current components, could be identified in the model plant Arabidopsis thaliana. Expression of the gene products in Xenopus oocytes confirmed the quick and slow current kinetics. In this study we provide an overview on our current knowledge on slow and quick anion channels in plants and analyze the molecular evolution of ALMT/QUAC-like and SLAC-like channels. We discovered fingerprints that allow screening databases for these channel types and were able to identify 192 (177 non-redundant) SLAC-like and 422 (402 non-redundant) ALMT/QUAC-like proteins in the fully sequenced genomes of 32 plant species. Phylogenetic analyses provided new insights into the molecular evolution of these channel types. We also combined sequence alignment and clustering with predictions of protein features, leading to the identification of known conserved phosphorylation sites in SLAC1-like channels along with potential sites that have not been yet experimentally confirmed. Using a similar strategy to analyze the hydropathicity of ALMT/QUAC-like channels, we propose a modified topology with additional transmembrane regions that integrates structure and function of these membrane proteins. Our results suggest that cross-referencing phylogenetic analyses with position-specific protein properties and functional data could be a very powerful tool for genome research approaches in general.},
  article-doi            = {10.3389/fpls.2012.00263},
  completed              = {20121212},
  electronic-publication = {20121129},
  history                = {2012/12/12 06:01 [medline]},
  keywords               = {ALMT, QUAC, SLAC/SLAH, anion channel, evolution, phosphorylation, topology, voltage dependent},
  language               = {eng},
  location-id            = {263},
  nlm-unique-id          = {101568200},
  owner                  = {NLM},
  publication-status     = {epublish},
  revised                = {20211021},
  source                 = {Front Plant Sci. 2012 Nov 29;3:263. doi: 10.3389/fpls.2012.00263. eCollection 2012.},
  status                 = {PubMed-not-MEDLINE},
  termowner              = {NOTNLM},
  title-abbreviation     = {Front Plant Sci},
}

@Article{GomezPorras2012,
  author                 = {Gomez-Porras, Judith Lucia and Riaño-Pachón, Diego Mauricio and Benito, Begoña and Haro, Rosario and Sklodowski, Kamil and Rodríguez-Navarro, Alonso and Dreyer, Ingo},
  journal                = {Frontiers in plant science},
  title                  = {Phylogenetic analysis of k(+) transporters in bryophytes, lycophytes, and flowering plants indicates a specialization of vascular plants.},
  year                   = {2012},
  pages                  = {167},
  volume                 = {3},
  electronic-issn        = {1664-462X},
  linking-issn           = {1664-462X},
  abstract               = {As heritage from early evolution, potassium (K(+)) is absolutely necessary for all living cells. It plays significant roles as stabilizer in metabolism and is important for enzyme activation, stabilization of protein synthesis, and neutralization of negative charges on cellular molecules as proteins and nucleic acids. Land plants even enlarged this spectrum of K(+) utilization after having gone ashore, despite the fact that K(+) is far less available in their new oligotrophic habitats than in sea water. Inevitably, plant cells had to improve and to develop unique transport systems for K(+) accumulation and distribution. In the past two decades a manifold of K(+) transporters from flowering plants has been identified at the molecular level. The recently published genome of the fern ally Selaginella moellendorffii now helps in providing a better understanding on the molecular changes involved in the colonization of land and the development of the vasculature and the seeds. In this article we present an inventory of K(+) transporters of this lycophyte and pigeonhole them together with their relatives from the moss Physcomitrella patens, the monocotyledon Oryza sativa, and two dicotyledonous species, the herbaceous plant Arabidopsis thaliana, and the tree Populus trichocarpa. Interestingly, the transition of green plants from an aqueous to a dry environment coincides with a dramatic reduction in the diversity of voltage-gated potassium channels followed by a diversification on the basis of one surviving K(+) channel class. The first appearance of K(+) release (K(out)) channels in S. moellendorffii that were shown in Arabidopsis to be involved in xylem loading and guard cell closure coincides with the specialization of vascular plants and may indicate an important adaptive step.},
  article-doi            = {10.3389/fpls.2012.00167},
  completed              = {20120823},
  electronic-publication = {20120802},
  history                = {2012/08/10 06:01 [medline]},
  keywords               = {Selaginella, channel, high-affinity, potassium, transport, voltage-dependent, voltage-independent},
  language               = {eng},
  location-id            = {167},
  nlm-unique-id          = {101568200},
  owner                  = {NLM},
  publication-status     = {epublish},
  revised                = {20211021},
  source                 = {Front Plant Sci. 2012 Aug 2;3:167. doi: 10.3389/fpls.2012.00167. eCollection 2012.},
  status                 = {PubMed-not-MEDLINE},
  termowner              = {NOTNLM},
  title-abbreviation     = {Front Plant Sci},
}

@Article{Winck2012,
  author                 = {Winck, Flavia V. and Riaño-Pachón, Diego Mauricio and Sommer, Frederik and Rupprecht, Jens and Mueller-Roeber, Bernd},
  journal                = {Proteomics},
  title                  = {The nuclear proteome of the green alga Chlamydomonas reinhardtii.},
  year                   = {2012},
  month                  = {Jan},
  pages                  = {95-100},
  volume                 = {12},
  electronic-issn        = {1615-9861},
  linking-issn           = {1615-9853},
  abstract               = {Nuclear proteins play a central role in regulating gene expression. Their identification is important for understanding how the nuclear repertoire changes over time under different conditions. Nuclear proteins are often underrepresented in proteomic studies due to the frequently low abundance of proteins involved in regulatory processes. So far, only few studies describing the nuclear proteome of plant species have been published. Recently, the genome sequence of the unicellular green alga Chlamydomonas reinhardtii has been obtained and annotated, allowing the development of further detailed studies for this organism. However, a detailed description of its nuclear proteome has not been reported so far. Here, we present an analysis of the nuclear proteome of the sequenced Chlamydomonas strain cc503. Using LC-MS/MS, we identified 672 proteins from nuclei isolates with a maximum 1% peptide spectrum false discovery rate. Besides well-known proteins (e.g. histones), transcription factors and other transcriptional regulators (e.g. tubby and HMG) were identified. The presence of protein motifs in nuclear proteins was investigated by computational tools, and specific over-represented protein motifs were identified. This study provides new insights into the complexity of the nuclear environment and reveals novel putative protein targets for further studies of nuclear mechanisms.},
  address                = {Germany},
  article-doi            = {10.1002/pmic.201000782},
  completed              = {20120424},
  electronic-publication = {20111209},
  history                = {2012/04/25 06:00 [medline]},
  issue                  = {1},
  keywords               = {Amino Acid Motifs, Amino Acid Sequence, Cell Nucleus/*metabolism, Chlamydomonas reinhardtii/*metabolism, Molecular Sequence Data, Peptide Fragments/chemistry, Plant Proteins/chemistry/*metabolism, Proteome/chemistry/*metabolism, Tandem Mass Spectrometry},
  language               = {eng},
  location-id            = {10.1002/pmic.201000782 [doi]},
  nlm-unique-id          = {101092707},
  owner                  = {NLM},
  publication-status     = {ppublish},
  registry-number        = {0 (Proteome)},
  revised                = {20120106},
  source                 = {Proteomics. 2012 Jan;12(1):95-100. doi: 10.1002/pmic.201000782. Epub 2011 Dec 9.},
  status                 = {MEDLINE},
  subset                 = {IM},
  title-abbreviation     = {Proteomics},
}

@Article{Rohrmann2011,
  author                 = {Rohrmann, Johannes and Tohge, Takayuki and Alba, Rob and Osorio, Sonia and Caldana, Camila and McQuinn, Ryan and Arvidsson, Samuel and van der Merwe, Margaretha J. and Riaño-Pachón, Diego Mauricio and Mueller-Roeber, Bernd and Fei, Zhangjun and Nesi, Adriano Nunes and Giovannoni, James J. and Fernie, Alisdair R.},
  journal                = {The Plant journal : for cell and molecular biology},
  title                  = {Combined transcription factor profiling, microarray analysis and metabolite profiling reveals the transcriptional control of metabolic shifts occurring during tomato fruit development.},
  year                   = {2011},
  month                  = {Dec},
  pages                  = {999-1013},
  volume                 = {68},
  abstract               = {Maturation of fleshy fruits such as tomato (Solanum lycopersicum) is subject to tight genetic control. Here we describe the development of a quantitative real-time PCR platform that allows accurate quantification of the expression level of approximately 1000 tomato transcription factors. In addition to utilizing this novel approach, we performed cDNA microarray analysis and metabolite profiling of primary and secondary metabolites using GC-MS and LC-MS, respectively. We applied these platforms to pericarp material harvested throughout fruit development, studying both wild-type Solanum lycopersicum cv. Ailsa Craig and the hp1 mutant. This mutant is functionally deficient in the tomato homologue of the negative regulator of the light signal transduction gene DDB1 from Arabidopsis, and is furthermore characterized by dramatically increased pigment and phenolic contents. We choose this particular mutant as it had previously been shown to have dramatic alterations in the content of several important fruit metabolites but relatively little impact on other ripening phenotypes. The combined dataset was mined in order to identify metabolites that were under the control of these transcription factors, and, where possible, the respective transcriptional regulation underlying this control. The results are discussed in terms of both programmed fruit ripening and development and the transcriptional and metabolic shifts that occur in parallel during these processes.},
  address                = {England},
  article-doi            = {10.1111/j.1365-313X.2011.04750.x},
  completed              = {20120504},
  electronic-issn        = {1365-313X},
  electronic-publication = {20111025},
  history                = {2012/05/05 06:00 [medline]},
  issue                  = {6},
  keywords               = {Fruit/*growth & development, *Gene Expression Profiling, *Gene Expression Regulation, Plant, *Genes, Lycopersicon esculentum/genetics/growth & development/*metabolism, Oligonucleotide Array Sequence Analysis, *Real-Time Polymerase Chain Reaction, Transcription Factors/genetics/*metabolism},
  language               = {eng},
  linking-issn           = {0960-7412},
  location-id            = {10.1111/j.1365-313X.2011.04750.x [doi]},
  nlm-unique-id          = {9207397},
  owner                  = {NLM},
  publication-status     = {ppublish},
  registry-number        = {0 (Transcription Factors)},
  revised                = {20111214},
  source                 = {Plant J. 2011 Dec;68(6):999-1013. doi: 10.1111/j.1365-313X.2011.04750.x. Epub 2011 Oct 25.},
  status                 = {MEDLINE},
  subset                 = {IM},
  title-abbreviation     = {Plant J},
}

@Article{Banks2011,
  author                 = {Banks, Jo Ann and Nishiyama, Tomoaki and Hasebe, Mitsuyasu and Bowman, John L. and Gribskov, Michael and dePamphilis, Claude and Albert, Victor A. and Aono, Naoki and Aoyama, Tsuyoshi and Ambrose, Barbara A. and Ashton, Neil W. and Axtell, Michael J. and Barker, Elizabeth and Barker, Michael S. and Bennetzen, Jeffrey L. and Bonawitz, Nicholas D. and Chapple, Clint and Cheng, Chaoyang and Correa, Luiz Gustavo Guedes and Dacre, Michael and DeBarry, Jeremy and Dreyer, Ingo and Elias, Marek and Engstrom, Eric M. and Estelle, Mark and Feng, Liang and Finet, Cédric and Floyd, Sandra K. and Frommer, Wolf B. and Fujita, Tomomichi and Gramzow, Lydia and Gutensohn, Michael and Harholt, Jesper and Hattori, Mitsuru and Heyl, Alexander and Hirai, Tadayoshi and Hiwatashi, Yuji and Ishikawa, Masaki and Iwata, Mineko and Karol, Kenneth G. and Koehler, Barbara and Kolukisaoglu, Uener and Kubo, Minoru and Kurata, Tetsuya and Lalonde, Sylvie and Li, Kejie and Li, Ying and Litt, Amy and Lyons, Eric and Manning, Gerard and Maruyama, Takeshi and Michael, Todd P. and Mikami, Koji and Miyazaki, Saori and Morinaga, Shin-ichi and Murata, Takashi and Mueller-Roeber, Bernd and Nelson, David R. and Obara, Mari and Oguri, Yasuko and Olmstead, Richard G. and Onodera, Naoko and Petersen, Bent Larsen and Pils, Birgit and Prigge, Michael and Rensing, Stefan A. and Riaño-Pachón, Diego Mauricio and Roberts, Alison W. and Sato, Yoshikatsu and Scheller, Henrik Vibe and Schulz, Burkhard and Schulz, Christian and Shakirov, Eugene V. and Shibagaki, Nakako and Shinohara, Naoki and Shippen, Dorothy E. and Sørensen, Iben and Sotooka, Ryo and Sugimoto, Nagisa and Sugita, Mamoru and Sumikawa, Naomi and Tanurdzic, Milos and Theissen, Günter and Ulvskov, Peter and Wakazuki, Sachiko and Weng, Jing-Ke and Willats, William W. G. T. and Wipf, Daniel and Wolf, Paul G. and Yang, Lixing and Zimmer, Andreas D. and Zhu, Qihui and Mitros, Therese and Hellsten, Uffe and Loqué, Dominique and Otillar, Robert and Salamov, Asaf and Schmutz, Jeremy and Shapiro, Harris and Lindquist, Erika and Lucas, Susan and Rokhsar, Daniel and Grigoriev, Igor V.},
  journal                = {Science (New York, N.Y.)},
  title                  = {The Selaginella genome identifies genetic changes associated with the evolution of vascular plants.},
  year                   = {2011},
  month                  = {May},
  pages                  = {960-3},
  volume                 = {332},
  abstract               = {Vascular plants appeared ~410 million years ago, then diverged into several lineages of which only two survive: the euphyllophytes (ferns and seed plants) and the lycophytes. We report here the genome sequence of the lycophyte Selaginella moellendorffii (Selaginella), the first nonseed vascular plant genome reported. By comparing gene content in evolutionarily diverse taxa, we found that the transition from a gametophyte- to a sporophyte-dominated life cycle required far fewer new genes than the transition from a nonseed vascular to a flowering plant, whereas secondary metabolic genes expanded extensively and in parallel in the lycophyte and angiosperm lineages. Selaginella differs in posttranscriptional gene regulation, including small RNA regulation of repetitive elements, an absence of the trans-acting small interfering RNA pathway, and extensive RNA editing of organellar genes.},
  article-doi            = {10.1126/science.1203810},
  article-pii            = {science.1203810},
  completed              = {20110603},
  electronic-issn        = {1095-9203},
  electronic-publication = {20110505},
  grantno                = {R01 HG004164/HG/NHGRI NIH HHS/United States},
  history                = {2011/06/04 06:00 [medline]},
  issue                  = {6032},
  keywords               = {*Biological Evolution, Bryopsida/genetics, Chlamydomonas/chemistry/genetics, DNA Transposable Elements, Evolution, Molecular, Gene Expression Regulation, Plant, Genes, *Genome, Magnoliopsida/chemistry/genetics, MicroRNAs/genetics, Molecular Sequence Data, Phylogeny, Plant Proteins/genetics/metabolism, Proteome/analysis, RNA Editing, RNA, Plant/genetics, Repetitive Sequences, Nucleic Acid, Selaginellaceae/*genetics/growth & development/metabolism, Sequence Analysis, DNA},
  language               = {eng},
  linking-issn           = {0036-8075},
  location-id            = {10.1126/science.1203810 [doi]},
  manuscript-id          = {NIHMS300873},
  nlm-unique-id          = {0404511},
  owner                  = {NLM},
  print-issn             = {0036-8075},
  publication-status     = {ppublish},
  registry-number        = {0 (RNA, Plant)},
  revised                = {20211020},
  second-id              = {GENBANK/HM173080},
  source                 = {Science. 2011 May 20;332(6032):960-3. doi: 10.1126/science.1203810. Epub 2011 May 5.},
  status                 = {MEDLINE},
  subset                 = {IM},
  title-abbreviation     = {Science},
}

@Article{Lang2010,
  author                 = {Lang, Daniel and Weiche, Benjamin and Timmerhaus, Gerrit and Richardt, Sandra and Riaño-Pachón, Diego Mauricio and Corrêa, Luiz G. G. and Reski, Ralf and Mueller-Roeber, Bernd and Rensing, Stefan A.},
  journal                = {Genome biology and evolution},
  title                  = {Genome-wide phylogenetic comparative analysis of plant transcriptional regulation: a timeline of loss, gain, expansion, and correlation with complexity.},
  year                   = {2010},
  month                  = {Jul},
  pages                  = {488-503},
  volume                 = {2},
  abstract               = {Evolutionary retention of duplicated genes encoding transcription-associated proteins (TAPs, comprising transcription factors and other transcriptional regulators) has been hypothesized to be positively correlated with increasing morphological complexity and paleopolyploidizations, especially within the plant kingdom. Here, we present the most comprehensive set of classification rules for TAPs and its application for genome-wide analyses of plants and algae. Using a dated species tree and phylogenetic comparative (PC) analyses, we define the timeline of TAP loss, gain, and expansion among Viridiplantae and find that two major bursts of gain/expansion occurred, coinciding with the water-to-land transition and the radiation of flowering plants. For the first time, we provide PC proof for the long-standing hypothesis that TAPs are major driving forces behind the evolution of morphological complexity, the latter in Plantae being shaped significantly by polyploidization and subsequent biased paleolog retention. Principal component analysis incorporating the number of TAPs per genome provides an alternate and significant proxy for complexity, ideally suited for PC genomics. Our work lays the ground for further interrogation of the shaping of gene regulatory networks underlying the evolution of organism complexity.},
  article-doi            = {10.1093/gbe/evq032},
  article-pii            = {evq032},
  completed              = {20101206},
  electronic-issn        = {1759-6653},
  electronic-publication = {20100719},
  history                = {2010/12/14 06:00 [medline]},
  keywords               = {Evolution, Molecular, Gene Duplication, Gene Expression Regulation, Plant, Genome, Genome-Wide Association Study, Markov Chains, MicroRNAs/genetics, Phylogeny, Plant Proteins/classification/genetics/metabolism, Plants/*genetics/metabolism, RNA, Plant/genetics, Time Factors, Transcription Factors/classification/genetics/metabolism, Transcription, Genetic},
  language               = {eng},
  linking-issn           = {1759-6653},
  location-id            = {10.1093/gbe/evq032 [doi]},
  nlm-unique-id          = {101509707},
  owner                  = {NLM},
  publication-status     = {epublish},
  registry-number        = {0 (Transcription Factors)},
  revised                = {20211020},
  source                 = {Genome Biol Evol. 2010 Jul 19;2:488-503. doi: 10.1093/gbe/evq032.},
  status                 = {MEDLINE},
  subset                 = {IM},
  title-abbreviation     = {Genome Biol Evol},
}

@Article{RianoPachon2010,
  author                 = {Riaño-Pachón, Diego Mauricio and Kleessen, Sabrina and Neigenfind, Jost and Durek, Pawel and Weber, Elke and Engelsberger, Wolfgang R. and Walther, Dirk and Selbig, Joachim and Schulze, Waltraud X. and Kersten, Birgit},
  journal                = {BMC genomics},
  title                  = {Proteome-wide survey of phosphorylation patterns affected by nuclear DNA polymorphisms in Arabidopsis thaliana.},
  year                   = {2010},
  month                  = {Jul},
  pages                  = {411},
  volume                 = {11},
  electronic-issn        = {1471-2164},
  linking-issn           = {1471-2164},
  abstract               = {BACKGROUND: Protein phosphorylation is an important post-translational modification influencing many aspects of dynamic cellular behavior. Site-specific phosphorylation of amino acid residues serine, threonine, and tyrosine can have profound effects on protein structure, activity, stability, and interaction with other biomolecules. Phosphorylation sites can be affected in diverse ways in members of any species, one such way is through single nucleotide polymorphisms (SNPs). The availability of large numbers of experimentally identified phosphorylation sites, and of natural variation datasets in Arabidopsis thaliana prompted us to analyze the effect of non-synonymous SNPs (nsSNPs) onto phosphorylation sites. RESULTS: From the analyses of 7,178 experimentally identified phosphorylation sites we found that: (i) Proteins with multiple phosphorylation sites occur more often than expected by chance. (ii) Phosphorylation hotspots show a preference to be located outside conserved domains. (iii) nsSNPs affected experimental phosphorylation sites as much as the corresponding non-phosphorylated amino acid residues. (iv) Losses of experimental phosphorylation sites by nsSNPs were identified in 86 A. thaliana proteins, among them receptor proteins were overrepresented.These results were confirmed by similar analyses of predicted phosphorylation sites in A. thaliana. In addition, predicted threonine phosphorylation sites showed a significant enrichment of nsSNPs towards asparagines and a significant depletion of the synonymous substitution. Proteins in which predicted phosphorylation sites were affected by nsSNPs (loss and gain), were determined to be mainly receptor proteins, stress response proteins and proteins involved in nucleotide and protein binding. Proteins involved in metabolism, catalytic activity and biosynthesis were less affected. CONCLUSIONS: We analyzed more than 7,100 experimentally identified phosphorylation sites in almost 4,300 protein-coding loci in silico, thus constituting the largest phosphoproteomics dataset for A. thaliana available to date. Our findings suggest a relatively high variability in the presence or absence of phosphorylation sites between different natural accessions in receptor and other proteins involved in signal transduction. Elucidating the effect of phosphorylation sites affected by nsSNPs on adaptive responses represents an exciting research goal for the future.},
  article-doi            = {10.1186/1471-2164-11-411},
  article-pii            = {1471-2164-11-411},
  completed              = {20100903},
  electronic-publication = {20100701},
  history                = {2010/09/04 06:00 [medline]},
  keywords               = {Amino Acid Sequence, Arabidopsis/cytology/*genetics/*metabolism, Binding Sites, Cell Nucleus/*genetics, DNA, Plant/*genetics, Humans, Molecular Sequence Data, Phosphorylation, Plant Proteins/chemistry/genetics/metabolism, *Polymorphism, Single Nucleotide, Proteome/chemistry/genetics/*metabolism},
  language               = {eng},
  location-id            = {10.1186/1471-2164-11-411 [doi]},
  nlm-unique-id          = {100965258},
  owner                  = {NLM},
  publication-status     = {epublish},
  registry-number        = {0 (Proteome)},
  revised                = {20211020},
  source                 = {BMC Genomics. 2010 Jul 1;11:411. doi: 10.1186/1471-2164-11-411.},
  status                 = {MEDLINE},
  subset                 = {IM},
  title-abbreviation     = {BMC Genomics},
}

@Article{PerezRodriguez2010,
  author                 = {Pérez-Rodríguez, Paulino and Riaño-Pachón, Diego Mauricio and Corrêa, Luiz Gustavo Guedes and Rensing, Stefan A. and Kersten, Birgit and Mueller-Roeber, Bernd},
  journal                = {Nucleic acids research},
  title                  = {PlnTFDB: updated content and new features of the plant transcription factor database.},
  year                   = {2010},
  month                  = {Jan},
  pages                  = {D822-7},
  volume                 = {38},
  abstract               = {The Plant Transcription Factor Database (PlnTFDB; http://plntfdb.bio.uni-potsdam.de/v3.0/) is an integrative database that provides putatively complete sets of transcription factors (TFs) and other transcriptional regulators (TRs) in plant species (sensu lato) whose genomes have been completely sequenced and annotated. The complete sets of 84 families of TFs and TRs from 19 species ranging from unicellular red and green algae to angiosperms are included in PlnTFDB, representing >1.6 billion years of evolution of gene regulatory networks. For each gene family, a basic description is provided that is complemented by literature references, and multiple sequence alignments of protein domains. TF or TR gene entries include information of expressed sequence tags, 3D protein structures of homologous proteins, domain architecture and cross-links to other computational resources online. Moreover, the different species in PlnTFDB are linked to each other by means of orthologous genes facilitating cross-species comparisons.},
  article-doi            = {10.1093/nar/gkp805},
  article-pii            = {gkp805},
  completed              = {20100201},
  electronic-issn        = {1362-4962},
  electronic-publication = {20091025},
  history                = {2010/02/02 06:00 [medline]},
  issue                  = {Database issue},
  keywords               = {Computational Biology/*methods/trends, *Databases, Genetic, Databases, Protein, Gene Expression Regulation, Plant, Gene Regulatory Networks, *Genes, Genome, Information Storage and Retrieval/methods, Internet, Plant Diseases/genetics, Plant Proteins/metabolism, Plants/*metabolism, Protein Structure, Tertiary, Software, Transcription Factors/*metabolism},
  language               = {eng},
  linking-issn           = {0305-1048},
  location-id            = {10.1093/nar/gkp805 [doi]},
  nlm-unique-id          = {0411011},
  owner                  = {NLM},
  print-issn             = {0305-1048},
  publication-status     = {ppublish},
  registry-number        = {0 (Transcription Factors)},
  revised                = {20211020},
  source                 = {Nucleic Acids Res. 2010 Jan;38(Database issue):D822-7. doi: 10.1093/nar/gkp805. Epub 2009 Oct 25.},
  status                 = {MEDLINE},
  subset                 = {IM},
  title-abbreviation     = {Nucleic Acids Res},
}

@Article{Arvidsson2008,
  author                 = {Arvidsson, Samuel and Kwasniewski, Miroslaw and Riaño-Pachón, Diego Mauricio and Mueller-Roeber, Bernd},
  journal                = {BMC bioinformatics},
  title                  = {QuantPrime--a flexible tool for reliable high-throughput primer design for quantitative PCR.},
  year                   = {2008},
  month                  = {Nov},
  pages                  = {465},
  volume                 = {9},
  electronic-issn        = {1471-2105},
  linking-issn           = {1471-2105},
  abstract               = {BACKGROUND: Medium- to large-scale expression profiling using quantitative polymerase chain reaction (qPCR) assays are becoming increasingly important in genomics research. A major bottleneck in experiment preparation is the design of specific primer pairs, where researchers have to make several informed choices, often outside their area of expertise. Using currently available primer design tools, several interactive decisions have to be made, resulting in lengthy design processes with varying qualities of the assays. RESULTS: Here we present QuantPrime, an intuitive and user-friendly, fully automated tool for primer pair design in small- to large-scale qPCR analyses. QuantPrime can be used online through the internet http://www.quantprime.de/ or on a local computer after download; it offers design and specificity checking with highly customizable parameters and is ready to use with many publicly available transcriptomes of important higher eukaryotic model organisms and plant crops (currently 295 species in total), while benefiting from exon-intron border and alternative splice variant information in available genome annotations. Experimental results with the model plant Arabidopsis thaliana, the crop Hordeum vulgare and the model green alga Chlamydomonas reinhardtii show success rates of designed primer pairs exceeding 96%. CONCLUSION: QuantPrime constitutes a flexible, fully automated web application for reliable primer design for use in larger qPCR experiments, as proven by experimental data. The flexible framework is also open for simple use in other quantification applications, such as hydrolyzation probe design for qPCR and oligonucleotide probe design for quantitative in situ hybridization. Future suggestions made by users can be easily implemented, thus allowing QuantPrime to be developed into a broad-range platform for the design of RNA expression assays.},
  article-doi            = {10.1186/1471-2105-9-465},
  article-pii            = {1471-2105-9-465},
  completed              = {20090805},
  electronic-publication = {20081101},
  history                = {2008/11/04 09:00 [entrez]},
  keywords               = {Base Sequence, *DNA Primers, Databases, Genetic, Internet, Molecular Sequence Data, Nucleic Acid Probes, Polymerase Chain Reaction/*methods, Sensitivity and Specificity, Sequence Analysis, DNA/*methods, *Software, User-Computer Interface},
  language               = {eng},
  location-id            = {10.1186/1471-2105-9-465 [doi]},
  nlm-unique-id          = {100965194},
  owner                  = {NLM},
  publication-status     = {epublish},
  registry-number        = {0 (Nucleic Acid Probes)},
  revised                = {20181113},
  source                 = {BMC Bioinformatics. 2008 Nov 1;9:465. doi: 10.1186/1471-2105-9-465.},
  status                 = {MEDLINE},
  subset                 = {IM},
  title-abbreviation     = {BMC Bioinformatics},
}

@Article{RianoPachon2009,
  author                 = {Riaño-Pachón, Diego Mauricio and Nagel, Axel and Neigenfind, Jost and Wagner, Robert and Basekow, Rico and Weber, Elke and Mueller-Roeber, Bernd and Diehl, Svenja and Kersten, Birgit},
  journal                = {Nucleic acids research},
  title                  = {GabiPD: the GABI primary database--a plant integrative 'omics' database.},
  year                   = {2009},
  month                  = {Jan},
  pages                  = {D954-9},
  volume                 = {37},
  abstract               = {The GABI Primary Database, GabiPD (http://www.gabipd.org/), was established in the frame of the German initiative for Genome Analysis of the Plant Biological System (GABI). The goal of GabiPD is to collect, integrate, analyze and visualize primary information from GABI projects. GabiPD constitutes a repository and analysis platform for a wide array of heterogeneous data from high-throughput experiments in several plant species. Data from different 'omics' fronts are incorporated (i.e. genomics, transcriptomics, proteomics and metabolomics), originating from 14 different model or crop species. We have developed the concept of GreenCards for text-based retrieval of all data types in GabiPD (e.g. clones, genes, mutant lines). All data types point to a central Gene GreenCard, where gene information is integrated from genome projects or NCBI UniGene sets. The centralized Gene GreenCard allows visualizing ESTs aligned to annotated transcripts as well as displaying identified protein domains and gene structure. Moreover, GabiPD makes available interactive genetic maps from potato and barley, and protein 2DE gels from Arabidopsis thaliana and Brassica napus. Gene expression and metabolic-profiling data can be visualized through MapManWeb. By the integration of complex data in a framework of existing knowledge, GabiPD provides new insights and allows for new interpretations of the data.},
  article-doi            = {10.1093/nar/gkn611},
  article-pii            = {gkn611},
  completed              = {20090303},
  electronic-issn        = {1362-4962},
  electronic-publication = {20080923},
  history                = {2009/03/04 09:00 [medline]},
  issue                  = {Database issue},
  keywords               = {*Databases, Genetic, Gene Expression Profiling, *Genes, Plant, *Genome, Metabolomics, Plant Proteins/chemistry/*genetics/metabolism, Plants/metabolism, Proteomics, Software, Systems Integration},
  language               = {eng},
  linking-issn           = {0305-1048},
  location-id            = {10.1093/nar/gkn611 [doi]},
  nlm-unique-id          = {0411011},
  owner                  = {NLM},
  print-issn             = {0305-1048},
  publication-status     = {ppublish},
  registry-number        = {0 (Plant Proteins)},
  revised                = {20181113},
  source                 = {Nucleic Acids Res. 2009 Jan;37(Database issue):D954-9. doi: 10.1093/nar/gkn611. Epub 2008 Sep 23.},
  status                 = {MEDLINE},
  subset                 = {IM},
  title-abbreviation     = {Nucleic Acids Res},
}

@Article{Balazadeh2008,
  author             = {Balazadeh, S. and Riaño-Pachón, Diego Mauricio and Mueller-Roeber, B.},
  journal            = {Plant biology (Stuttgart, Germany)},
  title              = {Transcription factors regulating leaf senescence in Arabidopsis thaliana.},
  year               = {2008},
  month              = {Sep},
  pages              = {63-75},
  volume             = {10 Suppl 1},
  linking-issn       = {1435-8603},
  print-issn         = {1435-8603},
  abstract           = {Senescence is a highly regulated process, eventually leading to cell and tissue disintegration: a physiological process associated with nutrient (e.g. nitrogen) redistribution from leaves to reproductive organs. Senescence is not observed in young leaves, indicating that repressors efficiently act to suppress cell degradation during early leaf development and/or that senescence activators are switched on when a leaf ages. Thus, massive regulatory network re-wiring likely constitutes an important component of the pre-senescence process. Transcription factors (TFs) have been shown to be central elements of such regulatory networks. Here, we used quantitative real-time polymerase chain reaction (qRT-PCR) analysis to study the expression of 1880 TF genes during pre-senescence and early-senescence stages of leaf development, using Arabidopsis thaliana as a model. We show that the expression of 185 TF genes changes when leaves develop from half to fully expanded leaves and finally enter partial senescence. Our analysis identified 41 TF genes that were gradually up-regulated as leaves progressed through these developmental stages. We also identified 144 TF genes that were down-regulated during senescence. A considerable number of the senescence-regulated TF genes were found to respond to abiotic stress, and salt stress appeared to be the major factor controlling their expression. Our data indicate a peculiar fine-tuning of developmental shifts during late-leaf development that is controlled by TFs.},
  address            = {England},
  article-doi        = {10.1111/j.1438-8677.2008.00088.x},
  article-pii        = {PLB088},
  completed          = {20081103},
  history            = {2008/09/20 09:00 [entrez]},
  keywords           = {Arabidopsis/*genetics/growth & development/physiology, Arabidopsis Proteins/genetics/*physiology, Cellular Senescence/*genetics, Gene Expression Profiling, Gene Expression Regulation, Plant, Oligonucleotide Array Sequence Analysis, Plant Leaves/genetics/growth & development/physiology, Reverse Transcriptase Polymerase Chain Reaction, Seeds/genetics/growth & development/physiology, Sodium Chloride/metabolism, Transcription Factors/genetics/*physiology, Water/metabolism},
  language           = {eng},
  location-id        = {10.1111/j.1438-8677.2008.00088.x [doi]},
  nlm-unique-id      = {101148926},
  owner              = {NLM},
  publication-status = {ppublish},
  registry-number    = {451W47IQ8X (Sodium Chloride)},
  revised            = {20171116},
  source             = {Plant Biol (Stuttg). 2008 Sep;10 Suppl 1:63-75. doi: 10.1111/j.1438-8677.2008.00088.x.},
  status             = {MEDLINE},
  subset             = {IM},
  title-abbreviation = {Plant Biol (Stuttg)},
}

@Article{Correa2008,
  author                 = {Corrêa, Luiz Gustavo Guedes and Riaño-Pachón, Diego Mauricio and Schrago, Carlos Guerra and dos Santos, Renato Vicentini and Mueller-Roeber, Bernd and Vincentz, Michel},
  journal                = {PloS one},
  title                  = {The role of bZIP transcription factors in green plant evolution: adaptive features emerging from four founder genes.},
  year                   = {2008},
  month                  = {Aug},
  pages                  = {e2944},
  volume                 = {3},
  electronic-issn        = {1932-6203},
  linking-issn           = {1932-6203},
  abstract               = {BACKGROUND: Transcription factors of the basic leucine zipper (bZIP) family control important processes in all eukaryotes. In plants, bZIPs are regulators of many central developmental and physiological processes including photomorphogenesis, leaf and seed formation, energy homeostasis, and abiotic and biotic stress responses. Here we performed a comprehensive phylogenetic analysis of bZIP genes from algae, mosses, ferns, gymnosperms and angiosperms. METHODOLOGY/PRINCIPAL FINDINGS: We identified 13 groups of bZIP homologues in angiosperms, three more than known before, that represent 34 Possible Groups of Orthologues (PoGOs). The 34 PoGOs may correspond to the complete set of ancestral angiosperm bZIP genes that participated in the diversification of flowering plants. Homologous genes dedicated to seed-related processes and ABA-mediated stress responses originated in the common ancestor of seed plants, and three groups of homologues emerged in the angiosperm lineage, of which one group plays a role in optimizing the use of energy. CONCLUSIONS/SIGNIFICANCE: Our data suggest that the ancestor of green plants possessed four bZIP genes functionally involved in oxidative stress and unfolded protein responses that are bZIP-mediated processes in all eukaryotes, but also in light-dependent regulations. The four founder genes amplified and diverged significantly, generating traits that benefited the colonization of new environments.},
  article-doi            = {10.1371/journal.pone.0002944},
  article-pii            = {08-PONE-RA-03672R3},
  completed              = {20081218},
  electronic-publication = {20080813},
  history                = {2008/08/14 09:00 [entrez]},
  issue                  = {8},
  keywords               = {Basic-Leucine Zipper Transcription Factors/genetics/*physiology, Evolution, Molecular, *Founder Effect, Gene Pool, *Genes, Plant, Genetic Carrier Screening, Genetic Variation, Magnoliopsida/genetics, Phylogeny, Plant Proteins/genetics/*physiology, Plants/classification/*genetics},
  language               = {eng},
  location-id            = {e2944},
  nlm-unique-id          = {101285081},
  owner                  = {NLM},
  publication-status     = {epublish},
  registry-number        = {0 (Plant Proteins)},
  revised                = {20211020},
  source                 = {PLoS One. 2008 Aug 13;3(8):e2944. doi: 10.1371/journal.pone.0002944.},
  status                 = {MEDLINE},
  subset                 = {IM},
  title-abbreviation     = {PLoS One},
}

@Article{RianoPachon2008,
  author             = {Riaño-Pachón, Diego Mauricio and Corrêa, Luiz Gustavo Guedes and Trejos-Espinosa, Raúl and Mueller-Roeber, Bernd},
  journal            = {Genetics},
  title              = {Green transcription factors: a chlamydomonas overview.},
  year               = {2008},
  month              = {May},
  pages              = {31-9},
  volume             = {179},
  linking-issn       = {0016-6731},
  print-issn         = {0016-6731},
  abstract           = {Transcription factors (TFs) control gene expression by interacting with cis-elements in target gene promoters. Transcription regulators (TRs) assist in controlling gene expression through interaction with TFs, chromatin remodeling, or other mechanisms. Both types of proteins thus constitute master controllers of dynamic transcriptional networks. To uncover such control elements in the photosynthetic green alga Chlamydomonas reinhardtii, we performed a comprehensive analysis of its genome sequence. In total, we identified 234 genes encoding 147 TFs and 87 TRs of approximately 40 families. The set of putative TFs and TRs, including their transcript and protein sequences, domain architectures, and supporting information about putative orthologs, is available at http://plntfdb.bio.uni-potsdam.de/v2.0/. Twelve of 34 plant-specific TF families were found in at least one algal species, indicating their early evolutionary origin. Twenty-two plant-specific TF families and one plant-specific TR family were not observed in algae, suggesting their specific association with developmental or physiological processes characteristic to multicellular plants. We also analyzed the occurrence of proteins that constitute the light-regulated transcriptional network in angiosperms and found putative algal orthologs for most of them. Our analysis provides a solid ground for future experimental studies aiming at deciphering the transcriptional regulatory networks in green algae.},
  article-doi        = {10.1534/genetics.107.086090},
  article-pii        = {gen179131},
  completed          = {20080922},
  history            = {2008/05/22 09:00 [entrez]},
  issue              = {1},
  keywords           = {Animals, Chlamydomonas reinhardtii/*genetics, Computational Biology, Genes, Protozoan/*genetics, Genomics, Magnoliopsida/*genetics, *Phylogeny, Species Specificity, Transcription Factors/*genetics},
  language           = {eng},
  location-id        = {10.1534/genetics.107.086090 [doi]},
  nlm-unique-id      = {0374636},
  owner              = {NLM},
  publication-status = {ppublish},
  registry-number    = {0 (Transcription Factors)},
  revised            = {20211020},
  source             = {Genetics. 2008 May;179(1):31-9. doi: 10.1534/genetics.107.086090.},
  status             = {MEDLINE},
  subset             = {IM},
  title-abbreviation = {Genetics},
}

@Article{Merchant2007,
  author             = {Merchant, Sabeeha S. and Prochnik, Simon E. and Vallon, Olivier and Harris, Elizabeth H. and Karpowicz, Steven J. and Witman, George B. and Terry, Astrid and Salamov, Asaf and Fritz-Laylin, Lillian K. and Maréchal-Drouard, Laurence and Marshall, Wallace F. and Qu, Liang-Hu and Nelson, David R. and Sanderfoot, Anton A. and Spalding, Martin H. and Kapitonov, Vladimir V. and Ren, Qinghu and Ferris, Patrick and Lindquist, Erika and Shapiro, Harris and Lucas, Susan M. and Grimwood, Jane and Schmutz, Jeremy and Cardol, Pierre and Cerutti, Heriberto and Chanfreau, Guillaume and Chen, Chun-Long and Cognat, Valérie and Croft, Martin T. and Dent, Rachel and Dutcher, Susan and Fernández, Emilio and Fukuzawa, Hideya and González-Ballester, David and González-Halphen, Diego and Hallmann, Armin and Hanikenne, Marc and Hippler, Michael and Inwood, William and Jabbari, Kamel and Kalanon, Ming and Kuras, Richard and Lefebvre, Paul A. and Lemaire, Stéphane D. and Lobanov, Alexey V. and Lohr, Martin and Manuell, Andrea and Meier, Iris and Mets, Laurens and Mittag, Maria and Mittelmeier, Telsa and Moroney, James V. and Moseley, Jeffrey and Napoli, Carolyn and Nedelcu, Aurora M. and Niyogi, Krishna and Novoselov, Sergey V. and Paulsen, Ian T. and Pazour, Greg and Purton, Saul and Ral, Jean-Philippe and Riaño-Pachón, Diego Mauricio and Riekhof, Wayne and Rymarquis, Linda and Schroda, Michael and Stern, David and Umen, James and Willows, Robert and Wilson, Nedra and Zimmer, Sara Lana and Allmer, Jens and Balk, Janneke and Bisova, Katerina and Chen, Chong-Jian and Elias, Marek and Gendler, Karla and Hauser, Charles and Lamb, Mary Rose and Ledford, Heidi and Long, Joanne C. and Minagawa, Jun and Page, M. Dudley and Pan, Junmin and Pootakham, Wirulda and Roje, Sanja and Rose, Annkatrin and Stahlberg, Eric and Terauchi, Aimee M. and Yang, Pinfen and Ball, Steven and Bowler, Chris and Dieckmann, Carol L. and Gladyshev, Vadim N. and Green, Pamela and Jorgensen, Richard and Mayfield, Stephen and Mueller-Roeber, Bernd and Rajamani, Sathish and Sayre, Richard T. and Brokstein, Peter and Dubchak, Inna and Goodstein, David and Hornick, Leila and Huang, Y. Wayne and Jhaveri, Jinal and Luo, Yigong and Martínez, Diego and Ngau, Wing Chi Abby and Otillar, Bobby and Poliakov, Alexander and Porter, Aaron and Szajkowski, Lukasz and Werner, Gregory and Zhou, Kemin and Grigoriev, Igor V. and Rokhsar, Daniel S. and Grossman, Arthur R.},
  journal            = {Science (New York, N.Y.)},
  title              = {The Chlamydomonas genome reveals the evolution of key animal and plant functions.},
  year               = {2007},
  month              = {Oct},
  pages              = {245-50},
  volume             = {318},
  abstract           = {Chlamydomonas reinhardtii is a unicellular green alga whose lineage diverged from land plants over 1 billion years ago. It is a model system for studying chloroplast-based photosynthesis, as well as the structure, assembly, and function of eukaryotic flagella (cilia), which were inherited from the common ancestor of plants and animals, but lost in land plants. We sequenced the approximately 120-megabase nuclear genome of Chlamydomonas and performed comparative phylogenomic analyses, identifying genes encoding uncharacterized proteins that are likely associated with the function and biogenesis of chloroplasts or eukaryotic flagella. Analyses of the Chlamydomonas genome advance our understanding of the ancestral eukaryotic cell, reveal previously unknown genes associated with photosynthetic and flagellar functions, and establish links between ciliopathy and the composition and function of flagella.},
  article-doi        = {10.1126/science.1143609},
  article-pii        = {318/5848/245},
  completed          = {20071025},
  electronic-issn    = {1095-9203},
  grantno            = {R01 GM062915-06/GM/NIGMS NIH HHS/United States},
  history            = {2007/10/13 09:00 [entrez]},
  issue              = {5848},
  keywords           = {Algal Proteins/*genetics/*physiology, Animals, *Biological Evolution, Chlamydomonas reinhardtii/*genetics/physiology, Chloroplasts/metabolism, Computational Biology, DNA, Algal/genetics, Flagella/metabolism, Genes, *Genome, Genomics, Membrane Transport Proteins/genetics/physiology, Molecular Sequence Data, Multigene Family, Photosynthesis/genetics, Phylogeny, Plants/genetics, Proteome, Sequence Analysis},
  language           = {eng},
  linking-issn       = {0036-8075},
  manuscript-id      = {NIHMS166705},
  nlm-unique-id      = {0404511},
  owner              = {NLM},
  print-issn         = {0036-8075},
  publication-status = {ppublish},
  registry-number    = {0 (Proteome)},
  revised            = {20211020},
  second-id          = {GENBANK/ABCN01000000},
  source             = {Science. 2007 Oct 12;318(5848):245-50. doi: 10.1126/science.1143609.},
  status             = {MEDLINE},
  subset             = {IM},
  title-abbreviation = {Science},
}

@Article{GomezPorras2007,
  author                 = {Gómez-Porras, Judith L. and Riaño-Pachón, Diego Mauricio and Dreyer, Ingo and Mayer, Jorge E. and Mueller-Roeber, Bernd},
  journal                = {BMC genomics},
  title                  = {Genome-wide analysis of ABA-responsive elements ABRE and CE3 reveals divergent patterns in Arabidopsis and rice.},
  year                   = {2007},
  month                  = {Aug},
  pages                  = {260},
  volume                 = {8},
  abstract               = {BACKGROUND: In plants, complex regulatory mechanisms are at the core of physiological and developmental processes. The phytohormone abscisic acid (ABA) is involved in the regulation of various such processes, including stomatal closure, seed and bud dormancy, and physiological responses to cold, drought and salinity stress. The underlying tissue or plant-wide control circuits often include combinatorial gene regulatory mechanisms and networks that we are only beginning to unravel with the help of new molecular tools. The increasing availability of genomic sequences and gene expression data enables us to dissect ABA regulatory mechanisms at the individual gene expression level. In this paper we used an in-silico-based approach directed towards genome-wide prediction and identification of specific features of ABA-responsive elements. In particular we analysed the genome-wide occurrence and positional arrangements of two well-described ABA-responsive cis-regulatory elements (CREs), ABRE and CE3, in thale cress (Arabidopsis thaliana) and rice (Oryza sativa). RESULTS: Our results show that Arabidopsis and rice use the ABA-responsive elements ABRE and CE3 distinctively. Earlier reports for various monocots have identified CE3 as a coupling element (CE) associated with ABRE. Surprisingly, we found that while ABRE is equally abundant in both species, CE3 is practically absent in Arabidopsis. ABRE-ABRE pairs are common in both genomes, suggesting that these can form functional ABA-responsive complexes (ABRCs) in Arabidopsis and rice. Furthermore, we detected distinct combinations, orientation patterns and DNA strand preferences of ABRE and CE3 motifs in rice gene promoters. CONCLUSION: Our computational analyses revealed distinct recruitment patterns of ABA-responsive CREs in upstream sequences of Arabidopsis and rice. The apparent absence of CE3s in Arabidopsis suggests that another CE pairs with ABRE to establish a functional ABRC capable of interacting with transcription factors. Further studies will be needed to test whether the observed differences are extrapolatable to monocots and dicots in general, and to understand how they contribute to the fine-tuning of the hormonal response. The outcome of our investigation can now be used to direct future experimentation designed to further dissect the ABA-dependent regulatory networks.},
  article-doi            = {10.1186/1471-2164-8-260},
  article-pii            = {1471-2164-8-260},
  completed              = {20071101},
  electronic-issn        = {1471-2164},
  electronic-publication = {20070801},
  history                = {2007/08/04 09:00 [entrez]},
  keywords               = {Abscisic Acid/*pharmacology, Arabidopsis/*genetics, Base Sequence, Chromosome Mapping/methods, Computational Biology, Gene Dosage, Gene Expression Regulation, Plant/*drug effects, Gene Order, Genes, Plant, *Genome, Molecular Sequence Data, Oryza/*genetics, Response Elements/*drug effects},
  language               = {eng},
  linking-issn           = {1471-2164},
  nlm-unique-id          = {100965258},
  owner                  = {NLM},
  publication-status     = {epublish},
  registry-number        = {72S9A8J5GW (Abscisic Acid)},
  revised                = {20181113},
  source                 = {BMC Genomics. 2007 Aug 1;8:260. doi: 10.1186/1471-2164-8-260.},
  status                 = {MEDLINE},
  subset                 = {IM},
  title-abbreviation     = {BMC Genomics},
}

@Article{RianoPachon2007,
  author                 = {Riaño-Pachón, Diego Mauricio and Ruzicic, Slobodan and Dreyer, Ingo and Mueller-Roeber, Bernd},
  journal                = {BMC bioinformatics},
  title                  = {PlnTFDB: an integrative plant transcription factor database.},
  year                   = {2007},
  month                  = {Feb},
  pages                  = {42},
  volume                 = {8},
  abstract               = {BACKGROUND: Transcription factors (TFs) are key regulatory proteins that enhance or repress the transcriptional rate of their target genes by binding to specific promoter regions (i.e. cis-acting elements) upon activation or de-activation of upstream signaling cascades. TFs thus constitute master control elements of dynamic transcriptional networks. TFs have fundamental roles in almost all biological processes (development, growth and response to environmental factors) and it is assumed that they play immensely important functions in the evolution of species. In plants, TFs have been employed to manipulate various types of metabolic, developmental and stress response pathways. Cross-species comparison and identification of regulatory modules and hence TFs is thought to become increasingly important for the rational design of new plant biomass. Up to now, however, no computational repository is available that provides access to the largely complete sets of transcription factors of sequenced plant genomes. DESCRIPTION: PlnTFDB is an integrative plant transcription factor database that provides a web interface to access large (close to complete) sets of transcription factors of several plant species, currently encompassing Arabidopsis thaliana (thale cress), Populus trichocarpa (poplar), Oryza sativa (rice), Chlamydomonas reinhardtii and Ostreococcus tauri. It also provides an access point to its daughter databases of a species-centered representation of transcription factors (OstreoTFDB, ChlamyTFDB, ArabTFDB, PoplarTFDB and RiceTFDB). Information including protein sequences, coding regions, genomic sequences, expressed sequence tags (ESTs), domain architecture and scientific literature is provided for each family. CONCLUSION: We have created lists of putatively complete sets of transcription factors and other transcriptional regulators for five plant genomes. They are publicly available through http://plntfdb.bio.uni-potsdam.de. Further data will be included in the future when the sequences of other plant genomes become available.},
  article-doi            = {10.1186/1471-2105-8-42},
  article-pii            = {1471-2105-8-42},
  completed              = {20070306},
  electronic-issn        = {1471-2105},
  electronic-publication = {20070207},
  history                = {2007/02/09 09:00 [entrez]},
  keywords               = {*Databases, Protein, Gene Expression Regulation, Plant, Gene Regulatory Networks, Genome, Plants/*genetics, Promoter Regions, Genetic, Sequence Alignment/methods, Transcription Factors/*genetics, User-Computer Interface},
  language               = {eng},
  linking-issn           = {1471-2105},
  nlm-unique-id          = {100965194},
  owner                  = {NLM},
  publication-status     = {epublish},
  registry-number        = {0 (Transcription Factors)},
  revised                = {20181113},
  source                 = {BMC Bioinformatics. 2007 Feb 7;8:42. doi: 10.1186/1471-2105-8-42.},
  status                 = {MEDLINE},
  subset                 = {IM},
  title-abbreviation     = {BMC Bioinformatics},
}

@Article{RianoPachon2005,
  author             = {Riaño-Pachón, Diego Mauricio and Dreyer, Ingo and Mueller-Roeber, Bernd},
  journal            = {The Plant journal : for cell and molecular biology},
  title              = {Orphan transcripts in Arabidopsis thaliana: identification of several hundred previously unrecognized genes.},
  year               = {2005},
  month              = {Jul},
  pages              = {205-12},
  volume             = {43},
  abstract           = {Expressed sequence tags (ESTs) represent a huge resource for the discovery of previously unknown genetic information and functional genome assignment. In this study we screened a collection of 178 292 ESTs from Arabidopsis thaliana by testing them against previously annotated genes of the Arabidopsis genome. We identified several hundreds of new transcripts that match the Arabidopsis genome at so far unassigned loci. The transcriptional activity of these loci was independently confirmed by comparison with the Salk Whole Genome Array Data. To a large extent, the newly identified transcriptionally active genomic regions do not encode 'classic' proteins, but instead generate non-coding RNAs and/or small peptide-coding RNAs of presently unknown biological function. More than 560 transcripts identified in this study are not represented by the Affymetrix GeneChip arrays currently widely used for expression profiling in A. thaliana. Our data strongly support the hypothesis that numerous previously unknown genes exist in the Arabidopsis genome.},
  address            = {England},
  article-doi        = {10.1111/j.1365-313X.2005.02438.x},
  article-pii        = {TPJ2438},
  completed          = {20050912},
  history            = {2005/07/07 09:00 [entrez]},
  issue              = {2},
  keywords           = {Arabidopsis/*genetics, Arabidopsis Proteins/genetics, Expressed Sequence Tags, *Gene Expression Profiling, Gene Expression Regulation, Plant, *Genes, RNA, Messenger, Transcription, Genetic},
  language           = {eng},
  linking-issn       = {0960-7412},
  nlm-unique-id      = {9207397},
  owner              = {NLM},
  print-issn         = {0960-7412},
  publication-status = {ppublish},
  registry-number    = {0 (RNA, Plant)},
  revised            = {20061115},
  source             = {Plant J. 2005 Jul;43(2):205-12. doi: 10.1111/j.1365-313X.2005.02438.x.},
  status             = {MEDLINE},
  subset             = {IM},
  title-abbreviation = {Plant J},
}

@Article{GonzalezSayer2022,
  author       = {González-Sayer, Sandra and Oggenfuss, Ursula and García, Ibonne and Aristizabal, Fabio and Croll, Daniel and Riaño-Pachon, Diego Mauricio},
  journal      = {Genetics and molecular biology},
  title        = {High-quality genome assembly of Pseudocercospora ulei the main threat to natural rubber trees.},
  year         = {2022},
  issn         = {1415-4757},
  pages        = {e50510051},
  volume       = {45},
  abstract     = {Pseudocercospora ulei is the causal agent of South American Leaf Blight (SALB), the main disease affecting Hevea brasiliensis rubber tree, a native species to the Amazon. Rubber tree is a major crop in South American countries and SALB disease control strategies would benefit from the availability of genomic resources for the fungal pathogen. Here, we assembled and annotated the P. ulei genome. Shotgun sequencing was performed using second and third generation sequencing technologies. We present the first P. ulei high-quality genome assembly, the largest among Mycosphaerellaceae, with 93.8 Mbp, comprising 215 scaffolds, an N50 of 2.8 Mbp and a BUSCO gene completeness of 97.5%. We identified 12,745 protein-coding gene models in the P. ulei genome with 756 genes encoding secreted proteins and 113 genes encoding effector candidates. Most of the genome (80%) is composed of repetitive elements dominated by retrotransposons of the Gypsy superfamily. P. ulei has the largest genome size among Mycosphaerellaceae, with the highest TE content. In conclusion, we have established essential genomic resources for a wide range of studies on P. ulei and related species.},
  country      = {Brazil},
  doi          = {10.1590/1678-4685-GMB-2021-0051},
  issn-linking = {1415-4757},
  issue        = {1},
  nlm-id       = {100883590},
  owner        = {NLM},
  pii          = {S1415-47572022000100802},
  pmid         = {35037932},
  pubmodel     = {Electronic-eCollection},
  pubstate     = {epublish},
  revised      = {2022-01-18},
}

@Article{Zuvanov2021,
  author          = {Zuvanov, Luíza and Basso Garcia, Ana Letycia and Correr, Fernando Henrique and Bizarria, Rodolfo and Filho, Ailton Pereira da Costa and da Costa, Alisson Hayasi and Thomaz, Andréa T. and Pinheiro, Ana Lucia Mendes and Riaño-Pachón, Diego Mauricio and Winck, Flavia Vischi and Esteves, Franciele Grego and Margarido, Gabriel Rodrigues Alves and Casagrande, Giovanna Maria Stanfoca and Frajacomo, Henrique Cordeiro and Martins, Leonardo and Cavalheiro, Mariana Feitosa and Grachet, Nathalia Graf and da Silva, Raniere Gaia Costa and Cerri, Ricardo and Ramos, Rommel Thiago Juca and Medeiros, Simone Daniela Sartorio de and Tavares, Thayana Vieira and Corrêa Dos Santos, Renato Augusto},
  journal         = {PLoS computational biology},
  title           = {The experience of teaching introductory programming skills to bioscientists in Brazil.},
  year            = {2021},
  issn            = {1553-7358},
  month           = nov,
  pages           = {e1009534},
  volume          = {17},
  abstract        = {Computational biology has gained traction as an independent scientific discipline over the last years in South America. However, there is still a growing need for bioscientists, from different backgrounds, with different levels, to acquire programming skills, which could reduce the time from data to insights and bridge communication between life scientists and computer scientists. Python is a programming language extensively used in bioinformatics and data science, which is particularly suitable for beginners. Here, we describe the conception, organization, and implementation of the Brazilian Python Workshop for Biological Data. This workshop has been organized by graduate and undergraduate students and supported, mostly in administrative matters, by experienced faculty members since 2017. The workshop was conceived for teaching bioscientists, mainly students in Brazil, on how to program in a biological context. The goal of this article was to share our experience with the 2020 edition of the workshop in its virtual format due to the Coronavirus Disease 2019 (COVID-19) pandemic and to compare and contrast this year's experience with the previous in-person editions. We described a hands-on and live coding workshop model for teaching introductory Python programming. We also highlighted the adaptations made from in-person to online format in 2020, the participants' assessment of learning progression, and general workshop management. Lastly, we provided a summary and reflections from our personal experiences from the workshops of the last 4 years. Our takeaways included the benefits of the learning from learners' feedback (LLF) that allowed us to improve the workshop in real time, in the short, and likely in the long term. We concluded that the Brazilian Python Workshop for Biological Data is a highly effective workshop model for teaching a programming language that allows bioscientists to go beyond an initial exploration of programming skills for data analysis in the medium to long term.},
  citation-subset = {IM},
  completed       = {2021-11-24},
  country         = {United States},
  doi             = {10.1371/journal.pcbi.1009534},
  issn-linking    = {1553-734X},
  issue           = {11},
  keywords        = {Brazil; COVID-19; Computational Biology, education; Curriculum; Education, Distance; Humans; Pandemics; Physical Distancing; Programming Languages},
  nlm-id          = {101238922},
  owner           = {NLM},
  pii             = {PCOMPBIOL-D-21-00913},
  pmc             = {PMC8584955},
  pmid            = {34762646},
  pubmodel        = {Electronic-eCollection},
  pubstate        = {epublish},
  revised         = {2021-11-24},
}

@Article{Estevam2022,
  author       = {Estevam, Beatriz Rodrigues and Riaño-Pachón, Diego Mauricio},
  journal      = {MethodsX},
  title        = {CoCoView - A codon conservation viewer via sequence logos.},
  year         = {2022},
  issn         = {2215-0161},
  pages        = {101803},
  volume       = {9},
  abstract     = {Sequence logos are a simple way to display a set of aligned sequences, and they are useful to identify conserved patterns. Since their introduction, several tools have been developed for generating these representations at the single residue level (amino acids or nucleotides). We have developed a tool to build sequence logos of protein-coding sequences at the codon level, allowing more accurate analysis of coding-sequences as they represent synonymous and non-synonymous changes instead of showing only changes that imply on amino acid substitutions. We built CoCoView on top of the Logomaker Python API. It creates codon sequence logos from a multiple sequence alignment of protein-coding sequences. Some properties of the data and the generated logos can be controlled by the end-users, such as data redundancy, plot type and alphabet color. • Split aligned sequences into codon positions; • For each position compute codon frequency and information content; • Use the computed information to plot the graphic.},
  country      = {Netherlands},
  doi          = {10.1016/j.mex.2022.101803},
  issn-linking = {2215-0161},
  keywords     = {Codons representation; Consensus sequence; Conserved patterns; Information theory},
  nlm-id       = {101639829},
  owner        = {NLM},
  pii          = {S2215-0161(22)00183-2},
  pmc          = {PMC9382315},
  pmid         = {35990812},
  pubmodel     = {Electronic-eCollection},
  pubstate     = {epublish},
  revised      = {2022-08-23},
}

@Article{Lima2022,
  author          = {Lima, Joni E. and Serezino, Luis H. D. and Alves, Melissa K. and Tagliaferro, André L. and Vitti, Marielle and Creste, Silvana and Riaño-Pachón, Diego Mauricio and Dos Santos, Renato V. and Figueira, Antonio},
  journal         = {Molecular genetics and genomics : MGG},
  title           = {Root nitrate uptake in sugarcane (Saccharum spp.) is modulated by transcriptional and presumably posttranscriptional regulation of the NRT2.1/NRT3.1 transport system.},
  year            = {2022},
  issn            = {1617-4623},
  month           = sep,
  pages           = {1403--1421},
  volume          = {297},
  abstract        = {Nitrate uptake in sugarcane roots is regulated at the transcriptional and posttranscriptional levels based on the physiological status of the plant and is likely a determinant mechanism for discrimination against nitrate. Sugarcane (Saccharum spp.) is one of the most suitable energy crops for biofuel feedstock, but the reduced recovery of nitrogen (N) fertilizer by sugarcane roots increases the crop carbon footprint. The low nitrogen use efficiency (NUE) of sugarcane has been associated with the significantly low nitrate uptake, which limits the utilization of the large amount of nitrate available in agricultural soils. To understand the regulation of nitrate uptake in sugarcane roots, we identified the major canonical nitrate transporter genes (NRTs-NITRATE TRANSPORTERS) and then determined their expression profiles in roots under contrasting N conditions. Correlation of gene expression with  N-nitrate uptake revealed that under N deprivation or inorganic N (ammonium or nitrate) supply in N-sufficient roots, the regulation of ScNRT2.1 and ScNRT3.1 expression is the predominant mechanism for the modulation of the activity of the nitrate high-affinity transport system. Conversely, in N-deficient roots, the induction of ScNRT2.1 and ScNRT3.1 transcription is not correlated with the marked repression of nitrate uptake in response to nitrate resupply or high N provision, which suggested the existence of a posttranscriptional regulatory mechanism. Our findings suggested that high-affinity nitrate uptake is regulated at the transcriptional and presumably at the posttranscriptional levels based on the physiological N status and that the regulation of NRT2.1 and NRT3.1 activity is likely a determinant mechanism for the discrimination against nitrate uptake observed in sugarcane roots, which contributes to the low NUE in this crop species.},
  citation-subset = {IM},
  country         = {Germany},
  doi             = {10.1007/s00438-022-01929-8},
  issn-linking    = {1617-4623},
  issue           = {5},
  keywords        = {Biofuel; Biomass; HATS; NPF; NRT; Nitrate transporters; Nitrogen use efficiency},
  nlm-id          = {101093320},
  owner           = {NLM},
  pii             = {10.1007/s00438-022-01929-8},
  pmid            = {35879567},
  pubmodel        = {Print-Electronic},
  pubstate        = {ppublish},
  revised         = {2022-08-29},
}

@Article{Oliveira2022,
  author          = {de Oliveira, Lauana Pereira and Navarro, Bruno Viana and de Jesus Pereira, João Pedro and Lopes, Adriana Rios and Martins, Marina C. M. and Riaño-Pachón, Diego Mauricio and Buckeridge, Marcos Silveira},
  journal         = {Scientific reports},
  title           = {Bioinformatic analyses to uncover genes involved in trehalose metabolism in the polyploid sugarcane.},
  year            = {2022},
  issn            = {2045-2322},
  month           = may,
  pages           = {7516},
  volume          = {12},
  abstract        = {Trehalose-6-phosphate (T6P) is an intermediate of trehalose biosynthesis that plays an essential role in plant metabolism and development. Here, we comprehensively analyzed sequences from enzymes of trehalose metabolism in sugarcane, one of the main crops used for bioenergy production. We identified protein domains, phylogeny, and in silico expression levels for all classes of enzymes. However, post-translational modifications and residues involved in catalysis and substrate binding were analyzed only in trehalose-6-phosphate synthase (TPS) sequences. We retrieved 71 putative full-length TPS, 93 trehalose-6-phosphate phosphatase (TPP), and 3 trehalase (TRE) of sugarcane, showing all their conserved domains, respectively. Putative TPS (Classes I and II) and TPP sugarcane sequences were categorized into well-known groups reported in the literature. We measured the expression levels of the sequences from one sugarcane leaf transcriptomic dataset. Furthermore, TPS Class I has specific N-glycosylation sites inserted in conserved motifs and carries catalytic and binding residues in its TPS domain. Some of these residues are mutated in TPS Class II members, which implies loss of enzyme activity. Our approach retrieved many homo(eo)logous sequences for genes involved in trehalose metabolism, paving the way to discover the role of T6P signaling in sugarcane.},
  chemicals       = {Trehalose, Glucosyltransferases, Trehalase},
  citation-subset = {IM},
  completed       = {2022-05-10},
  country         = {England},
  doi             = {10.1038/s41598-022-11508-x},
  issn-linking    = {2045-2322},
  issue           = {1},
  keywords        = {Computational Biology; Glucosyltransferases, metabolism; Polyploidy; Saccharum, genetics, metabolism; Trehalase, genetics; Trehalose, genetics, metabolism},
  nlm-id          = {101563288},
  owner           = {NLM},
  pii             = {10.1038/s41598-022-11508-x},
  pmc             = {PMC9079074},
  pmid            = {35525890},
  pubmodel        = {Electronic},
  pubstate        = {epublish},
  revised         = {2022-07-16},
}

@Article{Paschoal2022,
  author          = {Paschoal, Daniele and Costa, Juliana L. and da Silva, Eder M. and da Silva, Fábia B. and Capelin, Diogo and Ometto, Vitor and Aricetti, Juliana A. and Carvalho, Gabriel G. and Pimpinato, Rodrigo F. and de Oliveira, Ricardo F. and Carrera, Esther and López-Díaz, Isabel and Rossi, Mônica L. and Tornisielo, Valdemar and Caldana, Camila and Riaño-Pachón, Diego Mauricio and Cesarino, Igor and Teixeira, Paulo J. P. L. and Figueira, Antonio},
  journal         = {Journal of experimental botany},
  title           = {Infection by Moniliophthora perniciosa reprograms tomato Micro-Tom physiology, establishes a sink, and increases secondary cell wall synthesis.},
  year            = {2022},
  issn            = {1460-2431},
  month           = jun,
  pages           = {3651--3670},
  volume          = {73},
  abstract        = {Witches' broom disease of cacao is caused by the pathogenic fungus Moniliophthora perniciosa. By using tomato (Solanum lycopersicum) cultivar Micro-Tom (MT) as a model system, we investigated the physiological and metabolic consequences of M. perniciosa infection to determine whether symptoms result from sink establishment during infection. Infection of MT by M. perniciosa caused reductions in root biomass and fruit yield, a decrease in leaf gas exchange, and down-regulation of photosynthesis-related genes. The total leaf area and water potential decreased, while ABA levels, water conductance/conductivity, and ABA-related gene expression increased. Genes related to sugar metabolism and those involved in secondary cell wall deposition were up-regulated upon infection, and the concentrations of sugars, fumarate, and amino acids increased. 14C-glucose was mobilized towards infected MT stems, but not in inoculated stems of the MT line overexpressing CYTOKININ OXIDASE-2 (35S::AtCKX2), suggesting a role for cytokinin in establishing a sugar sink. The up-regulation of genes involved in cell wall deposition and phenylpropanoid metabolism in infected MT, but not in 35S::AtCKX2 plants, suggests establishment of a cytokinin-mediated sink that promotes tissue overgrowth with an increase in lignin. Possibly, M. perniciosa could benefit from the accumulation of secondary cell walls during its saprotrophic phase of infection.},
  chemicals       = {Cytokinins, Sugars, Water},
  citation-subset = {IM},
  country         = {England},
  doi             = {10.1093/jxb/erac057},
  issn-linking    = {0022-0957},
  issue           = {11},
  keywords        = {Agaricales, genetics; Cacao, genetics; Cell Wall; Cytokinins; Lycopersicon esculentum, genetics, microbiology; Plant Diseases, microbiology; Sugars; Water; Theobroma cacao ; Cacao; cytokinin; lignin; saprotrophic; sugar; witches’ broom disease},
  nlm-id          = {9882906},
  owner           = {NLM},
  pii             = {6530360},
  pmid            = {35176760},
  pubmodel        = {Print},
  pubstate        = {ppublish},
  revised         = {2022-08-03},
}

@Article{RianoPachon2021,
  author          = {Riaño-Pachón, Diego Mauricio and Espitia-Navarro, Hector Fabio and Riascos, John Jaime and Margarido, Gabriel Rodrigues Alves},
  journal         = {Advances in experimental medicine and biology},
  title           = {Modern Approaches for Transcriptome Analyses in Plants.},
  year            = {2021},
  issn            = {0065-2598},
  pages           = {11--50},
  volume          = {1346},
  abstract        = {The collection of all transcripts in a cell, a tissue, or an organism is called the transcriptome, or meta-transcriptome when dealing with the transcripts of a community of different organisms. Nowadays, we have a vast array of technologies that allow us to assess the (meta-)transcriptome regarding its composition (which transcripts are produced) and the abundance of its components (what are the expression levels of each transcript), and we can do this across several samples, conditions, and time-points, at costs that are decreasing year after year, allowing experimental designs with ever-increasing complexity. Here we will present the current state of the art regarding the technologies that can be applied to the study of plant transcriptomes and their applications, including differential gene expression and coexpression analyses, identification of sequence polymorphisms, the application of machine learning for the identification of alternative splicing and ncRNAs, and the ranking of candidate genes for downstream studies. We continue with a collection of examples of these approaches in a diverse array of plant species to generate gene/transcript catalogs/atlases, population mapping, identification of genes related to stress phenotypes, and phylogenomics. We finalize the chapter with some of our ideas about the future of this dynamic field in plant physiology.},
  citation-subset = {IM},
  completed       = {2022-02-07},
  country         = {United States},
  doi             = {10.1007/978-3-030-80352-0_2},
  issn-linking    = {0065-2598},
  keywords        = {Alternative Splicing; Gene Expression Profiling; High-Throughput Nucleotide Sequencing; Plants, genetics; Sequence Analysis, RNA; Transcriptome; Assembly; Crops; Gene expression; Long reads; Next-generation sequencing; Polyploidy; RNA-Seq; Short reads; Transcription},
  nlm-id          = {0121103},
  owner           = {NLM},
  pmid            = {35113394},
  pubmodel        = {Print},
  pubstate        = {ppublish},
  revised         = {2022-05-31},
}

@Comment{jabref-meta: databaseType:bibtex;}