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Assessing the impact of comparative genomic sequence data on the functional annotation of the Drosophila genome

Casey M Bergman19, Barret D Pfeiffer19, Diego E Rincón-Limas26, Roger A Hoskins1, Andreas Gnirke3, Chris J Mungall4, Adrienne M Wang17, Brent Kronmiller18, Joanne Pacleb1, Soo Park1, Mark Stapleton1, Kenneth Wan1, Reed A George1, Pieter J de Jong5, Juan Botas2, Gerald M Rubin14 and Susan E Celniker1*

Author Affiliations

1 Berkeley Drosophila Genome Project, Lawrence Berkeley National Laboratory, One Cyclotron Road, Berkeley, CA 94720, USA

2 Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA

3 Exelixis Inc., South San Francisco, CA 94080, USA

4 Howard Hughes Medical Institute, Department of Molecular and Cellular Biology, University of California, Berkeley, CA 94720, USA

5 Children's Hospital and Research Center at Oakland, Oakland, CA 94609, USA

6 Current address: Departamento de Biologia Molecular, Universidad Autonoma de Tamaulipas-UAMRA, Reynosa, CP 88740, Mexico

7 Current address: Department of Physiology, University of California, San Francisco, CA 94143, USA

8 Current address: Department of Bioinformatics and Computational Biology, Iowa State University, Ames, IA 50011, USA

9 These authors contributed equally to this work

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Genome Biology 2002, 3:research0086-0086.20  doi:10.1186/gb-2002-3-12-research0086

This article is part of a series of refereed research articles from Berkeley Drosophila Genome Project, FlyBase and colleagues, describing Release 3 of the Drosophila genome, which are freely available at

Published: 30 December 2002



It is widely accepted that comparative sequence data can aid the functional annotation of genome sequences; however, the most informative species and features of genome evolution for comparison remain to be determined.


We analyzed conservation in eight genomic regions (apterous, even-skipped, fushi tarazu, twist, and Rhodopsins 1, 2, 3 and 4) from four Drosophila species (D. erecta, D. pseudoobscura, D. willistoni, and D. littoralis) covering more than 500 kb of the D. melanogaster genome. All D. melanogaster genes (and 78-82% of coding exons) identified in divergent species such as D. pseudoobscura show evidence of functional constraint. Addition of a third species can reveal functional constraint in otherwise non-significant pairwise exon comparisons. Microsynteny is largely conserved, with rearrangement breakpoints, novel transposable element insertions, and gene transpositions occurring in similar numbers. Rates of amino-acid substitution are higher in uncharacterized genes relative to genes that have previously been studied. Conserved non-coding sequences (CNCSs) tend to be spatially clustered with conserved spacing between CNCSs, and clusters of CNCSs can be used to predict enhancer sequences.


Our results provide the basis for choosing species whose genome sequences would be most useful in aiding the functional annotation of coding and cis-regulatory sequences in Drosophila. Furthermore, this work shows how decoding the spatial organization of conserved sequences, such as the clustering of CNCSs, can complement efforts to annotate eukaryotic genomes on the basis of sequence conservation alone.