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Comparative Validation of the D. melanogaster modENCODE transcriptome annotation

Friday, November 08, 2013 — Poster Session III

10:00 a.m. – 12:00 p.m.

FAES Academic Center (Upper-Level Terrace)




  • ZX. Chen
  • D. Sturgill
  • C.J. Qu
  • H. Jiang
  • S. Park
  • N. Boley
  • A.M. Suzuki
  • A.R. Fletcher
  • D. Plachetzki
  • P. FitzGerald
  • C. Artieri
  • J. Atallah
  • O. Barmina
  • J.B. Brown
  • K. Blankerburg
  • A. Dasgupta
  • S. Gubbala
  • S.E. Celniker
  • B. Oliver
  • S. Richards


The model organism Encyclopedia of DNA Elements project (modENCODE) has comprehensively re-annotated the D. melanogaster genome based on deep and diverse high-throughput data. We report that the vast majority of elements in the annotation are evolutionarily conserved, indicating that the annotation will be an important springboard for functional genetic testing by the Drosophila community. Since transcriptional activity that has been evolutionarily conserved is likely to have an advantageous function, we have performed large-scale interspecific comparisons to increase confidence in predicted annotations. To support comparative genomics, we filled in divergence gaps in the Drosophila phylogeny by generating draft genomes for eight new species. For comparative transcriptome analysis, we generated mRNA expression profiles on 81 samples from multiple tissues and developmental stages of 15 Drosophila species. To investigate conservation of transcription start sites, we performed cap analysis of gene expression in D. pseudoobscura. We found strikingly conserved sequence, expression, and splicing for the vast majority of transcript models in D. melanogaster modENCODE annotation, indicating that these transcripts are almost entirely functional. Overall, each type of genomic feature shows a characteristic divergence rate, highlighting the value of multi-species alignment in annotating a target genome.

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