Comparative analysis of chimpanzee and human y chromosomes unveils complex evolutionary pathway

Yoko Kuroki, Atsushi Toyoda, Hideki Noguchi, Todd D. Taylor, Takehiko Itoh, Dae Soo Kim, Dae Won Kim, Sang Haeng Choi, Il Chul Kim, Han Ho Choi, Yong Sung Kim, Yoko Satta, Naruya Saitou, Tomoyuki Yamada, Shinichi Morishita, Masahira Hattori, Yoshiyuki Sakaki, Hong Seog Park*, Asao Fujiyama

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

98 Citations (Scopus)


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.

Original languageEnglish
Pages (from-to)1-10
Number of pages10
JournalNature Genetics
Issue number2
Publication statusPublished - 2006
Externally publishedYes

ASJC Scopus subject areas

  • Genetics


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