TY  - JOUR
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
Y1  - 2005/01/01 
JF  - Genome Research 
JO  - Genome Research 
SP  - 1 
EP  - 18 
DO  - 10.1101/gr.3059305 
VL  - 15 
IS  - 1 
UR  - http://genome.cshlp.org/content/15/1/1.abstract 
N2  - 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. 
ER  -