Comparative genome sequencing of Drosophila pseudoobscura: chromosomal, gene, and cis-element evolution.
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.
Richards
Stephen
S
Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston Texas 77030, USA. stephenr@bcm.tmc.edu
Liu
Yue
Y
Bettencourt
Brian R
BR
Hradecky
Pavel
P
Letovsky
Stan
S
Nielsen
Rasmus
R
Thornton
Kevin
K
Hubisz
Melissa J
MJ
Chen
Rui
R
Meisel
Richard P
RP
Couronne
Olivier
O
Hua
Sujun
S
Smith
Mark A
MA
Zhang
Peili
P
Liu
Jing
J
Bussemaker
Harmen J
HJ
van Batenburg
Marinus F
MF
Howells
Sally L
SL
Scherer
Steven E
SE
Sodergren
Erica
E
Matthews
Beverly B
BB
Crosby
Madeline A
MA
Schroeder
Andrew J
AJ
Ortiz-Barrientos
Daniel
D
Rives
Catharine M
CM
Metzker
Michael L
ML
Muzny
Donna M
DM
Scott
Graham
G
Steffen
David
D
Wheeler
David A
DA
Worley
Kim C
KC
Havlak
Paul
P
Durbin
K James
KJ
Egan
Amy
A
Gill
Rachel
R
Hume
Jennifer
J
Morgan
Margaret B
MB
Miner
George
G
Hamilton
Cerissa
C
Huang
Yanmei
Y
Waldron
Lenée
L
Verduzco
Daniel
D
Clerc-Blankenburg
Kerstin P
KP
Dubchak
Inna
I
Noor
Mohamed A F
MA
Anderson
Wyatt
W
White
Kevin P
KP
Clark
Andrew G
AG
Schaeffer
Stephen W
SW
Gelbart
William
W
Weinstock
George M
GM
Gibbs
Richard A
RA
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*