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GENETICS
A computational and experimental approach to validating annotations and gene predictions in the Drosophila melanogaster genome

Mark Yandell ^* , , Adina M. Bailey ^, , Sima Misra ^, , ShengQiang Shu , Colin Wiel , Martha Evans-Holm , Susan E. Celniker ^¶, and Gerald M. Rubin ^*, , ¶

^*Howard Hughes Medical Institute and Department of Molecular and Cell Biology, University of California, Life Sciences Addition, Berkeley, CA 94720-3200; and ^¶Department of Genome Sciences, Lawrence Berkeley National Laboratory, One Cyclotron Road, Mailstop 64-121, Berkeley, CA 94720

Contributed by Gerald M. Rubin, December 17, 2004

Five years after the completion of the sequence of the Drosophila melanogaster genome, the number of protein-coding genes it contains remains a matter of debate; the number of computational gene predictions greatly exceeds the number of validated gene annotations. We have assembled a collection of >10,000 gene predictions that do not overlap existing gene annotations and have developed a process for their validation that allows us to efficiently prioritize and experimentally validate predictions from various sources by sequencing RT-PCR products to confirm gene structures. Our data provide experimental evidence for 122 protein-coding genes. Our analyses suggest that the entire collection of predictions contains only 700 additional protein-coding genes. Although we cannot rule out the discovery of genes with unusual features that make them refractory to existing methods, our results suggest that the D. melanogaster genome contains 14,000 protein-coding genes.

gene number | validation | genome annotation

Abbreviations: Mb, megabases; oligo, oligonucleotide; sjc, splice-junction conserved.

Data deposition: The sequences reported in this paper have been deposited in the GenBank database (accession nos. CX309415–CX309654).

M.Y., A.M.B., and S.M. contributed equally to this work.

To whom correspondence should be addressed at: Department of Molecular and Cell Biology, University of California, Life Sciences Addition, Room 539, Berkeley, CA 94720-3200. E-mail: myandell{at}fruitfly.org.

© 2005 by The National Academy of Sciences of the USA

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