title: Comparative genome sequencing of Drosophila pseudoobscura: chromosomal, gene, and cis-element evolution.
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.
authors.affiliation: Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston Texas 77030, USA. stephenr@bcm.tmc.edu
authors.forename: Stephen
authors.initials: S
authors.lastname: Richards
authors.forename: Yue
authors.initials: Y
authors.lastname: Liu
authors.forename: Brian R
authors.initials: BR
authors.lastname: Bettencourt
authors.forename: Pavel
authors.initials: P
authors.lastname: Hradecky
authors.forename: Stan
authors.initials: S
authors.lastname: Letovsky
authors.forename: Rasmus
authors.initials: R
authors.lastname: Nielsen
authors.forename: Kevin
authors.initials: K
authors.lastname: Thornton
authors.forename: Melissa J
authors.initials: MJ
authors.lastname: Hubisz
authors.forename: Rui
authors.initials: R
authors.lastname: Chen
authors.forename: Richard P
authors.initials: RP
authors.lastname: Meisel
authors.forename: Olivier
authors.initials: O
authors.lastname: Couronne
authors.forename: Sujun
authors.initials: S
authors.lastname: Hua
authors.forename: Mark A
authors.initials: MA
authors.lastname: Smith
authors.forename: Peili
authors.initials: P
authors.lastname: Zhang
authors.forename: Jing
authors.initials: J
authors.lastname: Liu
authors.forename: Harmen J
authors.initials: HJ
authors.lastname: Bussemaker
authors.forename: Marinus F
authors.initials: MF
authors.lastname: van Batenburg
authors.forename: Sally L
authors.initials: SL
authors.lastname: Howells
authors.forename: Steven E
authors.initials: SE
authors.lastname: Scherer
authors.forename: Erica
authors.initials: E
authors.lastname: Sodergren
authors.forename: Beverly B
authors.initials: BB
authors.lastname: Matthews
authors.forename: Madeline A
authors.initials: MA
authors.lastname: Crosby
authors.forename: Andrew J
authors.initials: AJ
authors.lastname: Schroeder
authors.forename: Daniel
authors.initials: D
authors.lastname: Ortiz-Barrientos
authors.forename: Catharine M
authors.initials: CM
authors.lastname: Rives
authors.forename: Michael L
authors.initials: ML
authors.lastname: Metzker
authors.forename: Donna M
authors.initials: DM
authors.lastname: Muzny
authors.forename: Graham
authors.initials: G
authors.lastname: Scott
authors.forename: David
authors.initials: D
authors.lastname: Steffen
authors.forename: David A
authors.initials: DA
authors.lastname: Wheeler
authors.forename: Kim C
authors.initials: KC
authors.lastname: Worley
authors.forename: Paul
authors.initials: P
authors.lastname: Havlak
authors.forename: K James
authors.initials: KJ
authors.lastname: Durbin
authors.forename: Amy
authors.initials: A
authors.lastname: Egan
authors.forename: Rachel
authors.initials: R
authors.lastname: Gill
authors.forename: Jennifer
authors.initials: J
authors.lastname: Hume
authors.forename: Margaret B
authors.initials: MB
authors.lastname: Morgan
authors.forename: George
authors.initials: G
authors.lastname: Miner
authors.forename: Cerissa
authors.initials: C
authors.lastname: Hamilton
authors.forename: Yanmei
authors.initials: Y
authors.lastname: Huang
authors.forename: Lenée
authors.initials: L
authors.lastname: Waldron
authors.forename: Daniel
authors.initials: D
authors.lastname: Verduzco
authors.forename: Kerstin P
authors.initials: KP
authors.lastname: Clerc-Blankenburg
authors.forename: Inna
authors.initials: I
authors.lastname: Dubchak
authors.forename: Mohamed A F
authors.initials: MA
authors.lastname: Noor
authors.forename: Wyatt
authors.initials: W
authors.lastname: Anderson
authors.forename: Kevin P
authors.initials: KP
authors.lastname: White
authors.forename: Andrew G
authors.initials: AG
authors.lastname: Clark
authors.forename: Stephen W
authors.initials: SW
authors.lastname: Schaeffer
authors.forename: William
authors.initials: W
authors.lastname: Gelbart
authors.forename: George M
authors.initials: GM
authors.lastname: Weinstock
authors.forename: Richard A
authors.initials: RA
authors.lastname: Gibbs
mesh_terms: D000818:Animals; D019457:Chromosome Breakage / Q000235:genetics; D007446:Chromosome Inversion / Q000235:genetics; D002874:Chromosome Mapping / Q000379:methods; D002875:Chromosomes / Q000235:genetics*; D017124:Conserved Sequence / Q000235:genetics; D004330:Drosophila / Q000235:genetics*; D004331:Drosophila melanogaster / Q000235:genetics; D004742:Enhancer Elements, Genetic; D019143:Evolution, Molecular; D015321:Gene Rearrangement / Q000235:genetics; D017344:Genes, Insect / Q000235:genetics*; D014644:Genetic Variation / Q000235:genetics; D016678:Genome; D008969:Molecular Sequence Data; D011237:Predictive Value of Tests; D012091:Repetitive Sequences, Nucleic Acid / Q000235:genetics; D017422:Sequence Analysis, DNA / Q000379:methods*