Re-annotation of eight Drosophila genomes

Abstract

The sequenced genomes of the Drosophila phylogeny are a central resource for comparative work supporting the understanding of the Drosophila melanogaster non-mammalian model system. These have also facilitated evolutionary studies on the selected and random differences that distinguish the thousands of extant species of Drosophila. However, full utility has been hampered by uneven genome annotation. We have generated a large expression profile dataset for nine species of Drosophila and trained a transcriptome assembly approach on D. melanogaster that best matched the extensively curated annotation. We then applied this to the other species to add more than 10000 transcript models per species. We also developed new orthologs to facilitate cross-species comparisons. We validated the new annotation of the distantly related Drosophila grimshawi with an extensive collection of newly sequenced cDNAs. This re-annotation will facilitate understanding both the core commonalities and the species differences in this important group of model organisms, and suggests a strategy for annotating the many forthcoming genomes covering the tree of life.