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

TitleComparative genome sequencing of Drosophila pseudoobscura: chromosomal, gene, and cis-element evolution.
Publication TypeJournal Article
Year of Publication2005
AuthorsRichards, 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
JournalGenome Res
Volume15
Issue1
Pagination1-18
Date Published2005 Jan
ISSN1088-9051
KeywordsAnimals, 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.

DOI10.1101/gr.3059305
Alternate JournalGenome Res.
PubMed ID15632085
PubMed Central IDPMC540289
Grant ListR01 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
U54 HG003273 / HG / NHGRI 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