Title | Comparative genome sequencing of Drosophila pseudoobscura: chromosomal, gene, and cis-element evolution. |
Publication Type | Journal Article |
Year of Publication | 2005 |
Authors | Richards, S, Liu, Y, Bettencourt, BR, Hradecky, P, Letovsky, S, Nielsen, R, Thornton, K, Hubisz, MJ, Chen, R, Meisel, RP, Couronne, O, Hua, S, Smith, MA, Zhang, P, 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, K Durbin, J, Egan, A, Gill, R, Hume, J, Morgan, MB, Miner, G, Hamilton, C, Huang, Y, Waldron, L, Verduzco, D, Clerc-Blankenburg, KP, Dubchak, I, Noor, MAF, Anderson, W, White, KP, Clark, AG, Schaeffer, SW, Gelbart, W, Weinstock, GM, Gibbs, RA |
Journal | Genome Res |
Volume | 15 |
Issue | 1 |
Pagination | 1-18 |
Date Published | 2005 Jan |
ISSN | 1088-9051 |
Keywords | Animals, Chromosome Breakage, Chromosome Inversion, Chromosome Mapping, Chromosomes, Conserved Sequence, Drosophila, Drosophila melanogaster, Enhancer Elements, Genetic, Evolution, Molecular, Gene Rearrangement, Genes, Insect, Genetic Variation, Genome, Molecular Sequence Data, Predictive Value of Tests, Repetitive Sequences, Nucleic Acid, Sequence Analysis, DNA |
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 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. |
DOI | 10.1101/gr.3059305 |
Alternate Journal | Genome Res |
PubMed ID | 15632085 |
PubMed Central ID | PMC540289 |
Grant List | R01 AI045402 / AI / NIAID NIH HHS / United States 5 P41 HG00739 / HG / NHGRI NIH HHS / United States 5 R37 GM28669 / GM / NIGMS NIH HHS / United States R37 GM028669 / GM / NIGMS NIH HHS / United States LM007276 / LM / NLM NIH HHS / United States P20 LM007276 / LM / NLM NIH HHS / United States GM-64590 / GM / NIGMS NIH HHS / United States AI-45402 / AI / NIAID NIH HHS / United States R01 GM064590 / GM / NIGMS NIH HHS / United States 1U01 HG02570 / HG / NHGRI NIH HHS / United States P41 HG000739 / HG / NHGRI NIH HHS / United States |
Comparative genome sequencing of Drosophila pseudoobscura: chromosomal, gene, and cis-element evolution.
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