Comparative genome sequencing of Drosophila pseudoobscura: Chromosomal, gene, and cis-element evolution

Stephen Richards, Yue Liu, Brian R. Bettencourt, Pavel Hradecky, Stan Letovsky, Rasmus Nielsen, Kevin Thornton, Melissa J. Hubisz, Rui Chen, Richard P. Meisel, Olivier Couronne, Sujun Hua, Mark A. Smith, Peili Zhang, Jing Liu, Harmen J. Bussemaker, Marinus F. van Batenburg, Sally L. Howells, Steven E. Scherer, Erica SodergreenBeverly B. Matthews, Madeline A. Crosby, Andrew J. Schroeder, Daniel Ortiz-Barrientos, Catharine M. Rives, Michael L. Metzker, Donna M. Muzny, Graham Scott, David Steffen, David A. Wheeler, Kim C. Worley, Paul Havlak, K. James Durbin, Amy Egan, Rachel Gill, Jennifer Hume, Margaret B. Morgan, George Miner, Cerissa Hamilton, Yanmei Huang, Lenée Waldron, Daniel Verduzco, Kerstin P. Clerc-Blankenburg, Inna Dubchak, Mohamed A.F. Noor, Wyatt Anderson, Kevin P. White, Andrew G. Clark, Stephen W. Schaeffer, William Gelbart, George M. Weinstock, Richard A. Gibbs

Research output: Contribution to journalArticlepeer-review

435 Scopus citations


We have sequenced the genome of a second Drosophila species, Drosophila pseudoobscura, and compared this to the genome sequence of Drosophila melanogaster, a primary model organism. Throughout evolution the vast majority of Drosophila genes have remained on the same chromosome arm, but within each arm gene order has been extensively reshuffled, leading to a minimum of 921 syntenic blocks shared between the species. A repetitive sequence is found in the D. pseudoobscura genome at many junctions between adjacent syntenic blocks. Analysis of this novel repetitive element family suggests that recombination between offset elements may have given rise to many paracentric inversions, thereby contributing to the shuffling of gene order in the D. pseudoobscura lineage. Based on sequence similarity and synteny, 10,516 putative orthologs have been identified as a core gene set conserved over 25-55 million years (Myr) since the pseudoobscura/ melanogaster divergence. Genes expressed in the testes had higher amino acid sequence divergence than the genome-wide average, consistent with the rapid evolution of sex-specific proteins. Cis-regulatory sequences are more conserved than random and nearby sequences between the species - but the difference is slight, suggesting that the evolution of cis-regulatory elements is flexible. Overall, a pattern of repeat-mediated chromosomal rearrangement, and high coadaptation of both male genes and cis-regulatory sequences emerges as important themes of genome divergence between these species of Drosophila.

Original languageEnglish (US)
Pages (from-to)1-18
Number of pages18
JournalGenome research
Issue number1
StatePublished - Jan 2005

All Science Journal Classification (ASJC) codes

  • Genetics
  • Genetics(clinical)


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