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

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

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Author Richards, Stephen
Liu, Yue
Bettencourt, Brian R.
Hradecky, Pavel
Letovsky, Stan
Nielsen, Rasmus
Thornton, Kevin
Hubisz, Melissa J.
Chen, Rui
Meisel, Richard P.
Couronne, Olivier
Hua, Sujun
Smith, Mark A.
Zhang, Peili
Liu, Jing
Bussemaker, Harmen J.
van Batenburg, Marinus F.
Howells, Sally L.
Scherer, Steven E.
Sodergren, Erica
Matthews, Beverly B.
Crosby, Madeline A.
Schroeder, Andrew J.
Ortiz-Barrientos, Daniel
Rives, Catharine M.
Metzker, Michael L.
Muzny, Donna M.
Scott, Graham
Steffen, David
Wheeler, David A.
Worley, Kim C.
Havlak, Paul
Durbin, K. James
Egan, Amy
Gill, Rachel
Hume, Jennifer
Morgan, Margaret B.
Miner, George
Hamilton, Cerissa
Huang, Yanmei
Waldron, Lenée
Verduzco, Daniel
Clerc-Blankenburg, Kerstin P.
Dubchak, Inna
Noor, Mohamed A.F.
Anderson, Wyatt
White, Kevin P.
Clark, Andrew G.
Schaeffer, Stephen W.
Gelbart, William
Weinstock, George M.
Gibbs, Richard A.
Title Comparative genome sequencing of Drosophila pseudoobscura: Chromosomal, gene, and cis-element evolution
Journal name Genome Research   Check publisher's open access policy
ISSN 1088-9051
Publication date 2005-01
Sub-type Article (original research)
DOI 10.1101/gr.3059305
Open Access Status DOI
Volume 15
Issue 1
Start page 1
End page 18
Total pages 18
Place of publication Cold Spring Harbor, NY, United States
Publisher Cold Spring Harbor Lab Press
Language eng
Abstract 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 A 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.
Keyword Biochemistry & Molecular Biology
Biotechnology & Applied Microbiology
Genetics & Heredity
Transposable Element
Regulatory Elements
Hobo Transposons
Mobile Elements
Species Group
Q-Index Code C1

Document type: Journal Article
Sub-type: Article (original research)
Collections: Excellence in Research Australia (ERA) - Collection
School of Biological Sciences Publications
Ecology Centre Publications
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Citation counts: TR Web of Science Citation Count  Cited 374 times in Thomson Reuters Web of Science Article | Citations
Scopus Citation Count Cited 353 times in Scopus Article | Citations
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