Nature Genetics 38, 158 - 167 (2006)
Published online: 1 January 2006; | doi:10.1038/ng1729
The HTML and PDF versions of this article were corrected on 29 January 2006. Please see the PDF for details.Comparative analysis of chimpanzee and human Y chromosomes unveils complex evolutionary pathwayYoko Kuroki1, Atsushi Toyoda1, Hideki Noguchi1, 2, Todd D Taylor1, Takehiko Itoh3, Dae-Soo Kim4, Dae-Won Kim4, 5, Sang-Haeng Choi4, Il-Chul Kim4, Han Ho Choi4, Yong Sung Kim4, Yoko Satta6, Naruya Saitou7, Tomoyuki Yamada2, Shinichi Morishita2, Masahira Hattori1, 8, Yoshiyuki Sakaki1, Hong-Seog Park4, 5
& Asao Fujiyama1, 91
RIKEN Genomic Sciences Center, Yokohama 230-0045, Japan. 2
Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa 277-0882, Japan. 3
Mitsubishi Research Institute, Tokyo 100-8141, Japan. 4
Genome Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 305-333, Korea. 5
University of Science and Technology, Daejeon 305-333, Korea. 6
The Graduate University for Advanced Studies, Hayama 240-0193, Japan. 7
National Institute of Genetics, Mishima 411-8540, Japan. 8
Kitasato University, Sagamihara 228-8555, Japan. 9
National Institute of Informatics, Tokyo 101-8430, Japan.
Correspondence should be addressed to Hong-Seog Park hspark@kribb.re.kr or Asao Fujiyama afujiyam@nii.ac.jp 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.
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