Annotation of the Drosophila melanogastereuchromatic genome: a systematic review

Sima Misra*, Madeline A. Crosby, Christopher J. Mungall, Beverley B. Matthews, Kathryn S. Campbell, Pavel Hradecky, Yanmei Huang, Joshua S. Kaminker, Gillian H. Millburn, Simon E. Prochnik, Christopher D. Smith, Jonathan L. Tupy, Eleanor J. Whitfield, Leyla Bayraktaroglu, Benjamin P. Berman, Brian R. Bettencourt, Susan E. Celniker, Aubrey Dnj de Grey, Rachel A. Drysdale, Nomi L. HarrisJohn Richter, Susan Russo, Andrew J. Schroeder, Sheng Qiang Shu, Mark Stapleton, Chihiro Yamada, Michael Ashburner, William M. Gelbart, Gerald M. Rubin, Suzanna E. Lewis

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

309 Scopus citations

Abstract

Background: The recent completion of the Drosophila melanogaster genomic sequence to high quality and the availability of a greatly expanded set of Drosophila cDNA sequences, aligning to 78% of the predicted euchromatic genes, afforded FlyBase the opportunity to significantly improve genomic annotations. We made the annotation process more rigorous by inspecting each gene visually, utilizing a comprehensive set of curation rules, requiring traceable evidence for each gene model, and comparing each predicted peptide to SWISS-PROT and TrEMBL sequences. Results: Although the number of predicted protein-coding genes in Drosophila remains essentially unchanged, the revised annotation significantly improves gene models, resulting in structural changes to 85% of the transcripts and 45% of the predicted proteins. We annotated transposable elements and non-protein-coding RNAs as new features, and extended the annotation of untranslated (UTR) sequences and alternative transcripts to include more than 70% and 20% of genes, respectively. Finally, cDNA sequence provided evidence for dicistronic transcripts, neighboring genes with overlapping UTRs on the same DNA sequence strand, alternatively spliced genes that encode distinct, non-overlapping peptides, and numerous nested genes. Conclusions: Identification of so many unusual gene models not only suggests that some mechanisms for gene regulation are more prevalent than previously believed, but also underscores the complex challenges of eukaryotic gene prediction. At present, experimental data and human curation remain essential to generate high-quality genome annotations.

Original languageAmerican English
Article numberresearch0083.1
JournalGenome Biology
Volume3
Issue number12
DOIs
StatePublished - Dec 2002
Externally publishedYes

Bibliographical note

Publisher Copyright:
© 2002, Misra et al., licensee BioMed Central Ltd.

Keywords

  • Additional Data File
  • Alternative Transcript
  • Nest Gene
  • Splice Junction
  • cDNA Data

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