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Shaun Jackman edited this page Aug 6, 2015 · 11 revisions

Genome

  • Sequencing
  • Assembly
    • Add methods text for assembly finishing Rene
  • Genome stats (size, GC content, coverage, et c.)
  • Protein coding genes
    • Inspect possible plastidial (psaA and psaB) and bacterial (bla) genes
  • rRNA genes
  • tRNA genes
  • Introns
    • Classify introns as group I or II
  • ORFs
  • Repeats

Transcriptome

  • Quantification, heat map and clustering
  • Compare expression of developing and mature tissues
  • Identify expressed ORFs
  • Annotate introns
  • Identify RNA editing sites
    • Identify created start codons

Comparative genomics

  • Compare chloroplast to Picea abies and Cycas taitungensis
  • Compare mitochondrion to Picea abies and Cycas taitungensis

Archive data

  • Submit genomes and annotations to GenBank

Open questions

  • Why is the mitochondrial genome so large?
    • Repeat expansion
    • Genome duplication
    • Genome acquisition
    • Nuclear gene transfer
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