title: Comparative analysis of chimpanzee and human Y chromosomes unveils complex evolutionary pathway.
abstract: The mammalian Y chromosome has unique characteristics compared with the autosomes or X chromosomes. Here we report the finished sequence of the chimpanzee Y chromosome (PTRY), including 271 kb of the Y-specific pseudoautosomal region 1 and 12.7 Mb of the male-specific region of the Y chromosome. Greater sequence divergence between the human Y chromosome (HSAY) and PTRY (1.78%) than between their respective whole genomes (1.23%) confirmed the accelerated evolutionary rate of the Y chromosome. Each of the 19 PTRY protein-coding genes analyzed had at least one nonsynonymous substitution, and 11 genes had higher nonsynonymous substitution rates than synonymous ones, suggesting relaxation of selective constraint, positive selection or both. We also identified lineage-specific changes, including deletion of a 200-kb fragment from the pericentromeric region of HSAY, expansion of young Alu families in HSAY and accumulation of young L1 elements and long terminal repeat retrotransposons in PTRY. Reconstruction of the common ancestral Y chromosome reflects the dynamic changes in our genomes in the 5-6 million years since speciation.
authors.affiliation: RIKEN Genomic Sciences Center, Yokohama 230-0045, Japan.
authors.forename: Yoko
authors.initials: Y
authors.lastname: Kuroki
authors.forename: Atsushi
authors.initials: A
authors.lastname: Toyoda
authors.forename: Hideki
authors.initials: H
authors.lastname: Noguchi
authors.forename: Todd D
authors.initials: TD
authors.lastname: Taylor
authors.forename: Takehiko
authors.initials: T
authors.lastname: Itoh
authors.forename: Dae-Soo
authors.initials: DS
authors.lastname: Kim
authors.forename: Dae-Won
authors.initials: DW
authors.lastname: Kim
authors.forename: Sang-Haeng
authors.initials: SH
authors.lastname: Choi
authors.forename: Il-Chul
authors.initials: IC
authors.lastname: Kim
authors.forename: Han Ho
authors.initials: HH
authors.lastname: Choi
authors.forename: Yong Sung
authors.initials: YS
authors.lastname: Kim
authors.forename: Yoko
authors.initials: Y
authors.lastname: Satta
authors.forename: Naruya
authors.initials: N
authors.lastname: Saitou
authors.forename: Tomoyuki
authors.initials: T
authors.lastname: Yamada
authors.forename: Shinichi
authors.initials: S
authors.lastname: Morishita
authors.forename: Masahira
authors.initials: M
authors.lastname: Hattori
authors.forename: Yoshiyuki
authors.initials: Y
authors.lastname: Sakaki
authors.forename: Hong-Seog
authors.initials: HS
authors.lastname: Park
authors.forename: Asao
authors.initials: A
authors.lastname: Fujiyama
mesh_terms: D000818:Animals; D041322:Chromosomes, Human, Y / Q000235:genetics*; D019143:Evolution, Molecular; D006801:Humans; D008297:Male; D008969:Molecular Sequence Data; D002679:Pan troglodytes / Q000235:genetics*; D012091:Repetitive Sequences, Nucleic Acid / Q000235:genetics; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA; D026801:Synteny / Q000235:genetics; D014998:Y Chromosome / Q000235:genetics*