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

被引:420
作者
Richards, S [1 ]
Liu, Y
Bettencourt, BR
Hradecky, P
Letovsky, S
Nielsen, R
Thornton, K
Hubisz, MJ
Chen, R
Meisel, RP
Couronne, O
Hua, SJ
Smith, MA
Zhang, PL
Liu, J
Bussemaker, HJ
van Batenburg, MF
Howells, SL
Scherer, SE
Sodergren, E
Matthews, BB
Crosby, MA
Schroeder, AJ
Ortiz-Barrientos, D
Rives, CM
Metzker, ML
Muzny, DM
Scott, G
Steffen, D
Wheeler, DA
Worley, KC
Havlak, P
Durbin, KJ
Egan, A
Gill, R
Hume, J
Morgan, MB
Miner, G
Hamilton, C
Huang, YM
Waldron, L
Verduzco, D
Clerc-Blankenburg, KP
Dubchak, I
Noor, MAF
Anderson, W
White, KP
Clark, AG
Schaeffer, SW
Gelbart, W
机构
[1] Baylor Coll Med, Human Genome Sequencing Ctr, Houston, TX 77030 USA
[2] Baylor Coll Med, Dept Mol & Human Genet, Houston, TX 77030 USA
[3] Baylor Coll Med, Program Struct & Computat Biol & Mol Biophys, Houston, TX 77030 USA
[4] Baylor Coll Med, WM Keck Ctr Computat Biol, Houston, TX 77030 USA
[5] Harvard Univ, Biol Labs, FlyBase Harvard, Dept Mol & Cellular Biol, Cambridge, MA 02138 USA
[6] Cornell Univ, Dept Biol Stat & Computat Biol, Ithaca, NY 14853 USA
[7] Cornell Univ, Dept Mol Biol & Genet, Ithaca, NY 14853 USA
[8] Penn State Univ, Intercoll Grad Degree Program Genet, University Pk, PA 16802 USA
[9] Penn State Univ, Dept Biol, University Pk, PA 16802 USA
[10] Penn State Univ, Inst Mol Evolut Genet, University Pk, PA 16802 USA
[11] Univ Calif Berkeley, Lawrence Berkeley Lab, Berkeley, CA 94720 USA
[12] Yale Univ, Sch Med, Dept Genet, New Haven, CT 06520 USA
[13] Columbia Univ, Dept Biol Sci, New York, NY 10027 USA
[14] Columbia Univ, Ctr Computat Biol & Bioinformat, New York, NY 10027 USA
[15] Louisiana State Univ, Dept Biol Sci, Baton Rouge, LA 70803 USA
[16] US Dept Energy Joint Genome Inst, Walnut Creek, CA 94598 USA
[17] Univ Amsterdam, Swammerdam Inst Life Sci, Amsterdam, Netherlands
[18] Univ Georgia, Dept Genet, Athens, GA 30602 USA
关键词
D O I
10.1101/gr.3059305
中图分类号
Q5 [生物化学]; Q7 [分子生物学];
学科分类号
071010 ; 081704 ;
摘要
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.
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页码:1 / 18
页数:18
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