RT Journal
A1 Richards, Stephen
A1 Liu, Yue
A1 Bettencourt, Brian R.
A1 Hradecky, Pavel
A1 Letovsky, Stan
A1 Nielsen, Rasmus
A1 Thornton, Kevin
A1 Hubisz, Melissa J.
A1 Chen, Rui
A1 Meisel, Richard P.
A1 Couronne, Olivier
A1 Hua, Sujun
A1 Smith, Mark A.
A1 Zhang, Peili
A1 Liu, Jing
A1 Bussemaker, Harmen J.
A1 van Batenburg, Marinus F.
A1 Howells, Sally L.
A1 Scherer, Steven E.
A1 Sodergren, Erica
A1 Matthews, Beverly B.
A1 Crosby, Madeline A.
A1 Schroeder, Andrew J.
A1 Ortiz-Barrientos, Daniel
A1 Rives, Catharine M.
A1 Metzker, Michael L.
A1 Muzny, Donna M.
A1 Scott, Graham
A1 Steffen, David
A1 Wheeler, David A.
A1 Worley, Kim C.
A1 Havlak, Paul
A1 Durbin, K. James
A1 Egan, Amy
A1 Gill, Rachel
A1 Hume, Jennifer
A1 Morgan, Margaret B.
A1 Miner, George
A1 Hamilton, Cerissa
A1 Huang, Yanmei
A1 Waldron, Lenée
A1 Verduzco, Daniel
A1 Clerc-Blankenburg, Kerstin P.
A1 Dubchak, Inna
A1 Noor, Mohamed A.F.
A1 Anderson, Wyatt
A1 White, Kevin P.
A1 Clark, Andrew G.
A1 Schaeffer, Stephen W.
A1 Gelbart, William
A1 Weinstock, George M.
A1 Gibbs, Richard A.
T1 Comparative genome sequencing of Drosophila pseudoobscura: Chromosomal, gene, and cis-element evolution
JF Genome Research 
JO Genome Research 
YR 2005 
FD January 01 
VO 15 
IS 1 
SP 1 
OP 18 
DO 10.1101/gr.3059305 
UL http://genome.cshlp.org/content/15/1/1.abstract 
AB 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.