Comparative analysis of chimpanzee and human Y chromosomes unveils complex evolutionary pathway Yoko Kuroki 1 , Atsushi Toyoda 1 , Hideki Noguchi 1,2 , Todd D Taylor 1 , Takehiko Itoh 3 , Dae-Soo Kim 4 , Dae-Won Kim 4,5 , Sang-Haeng Choi 4 , Il-Chul Kim 4 , Han Ho Choi 4 , Yong Sung Kim 4 , Yoko Satta 6 , Naruya Saitou 7 , Tomoyuki Yamada 2 , Shinichi Morishita 2 , Masahira Hattori 1,8 , Yoshiyuki Sakaki 1 , Hong-Seog Park 4,5 & Asao Fujiyama 1,9 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. The completion of the sequencing of the human genome has demon- strated the importance of comparative studies for deciphering the information and functions written in our genomes 1,2 . As chimpanzees are evolutionarily the closest living species to humans, various studies 3–11 have aimed to understand the genetic basis of the similar- ities and differences between the two species. Sequence-based genome- wide studies have defined with precision the nucleotide difference between human and chimpanzee as 1.23% (refs. 4,5,8). Owing to this high similarity in the sequences, it was essential to produce high- quality sequence data in order to delineate species-specific changes accumulated after the species diverged 10 . The mammalian sex chromosomes are thought to have originated from a pair of autosomes that ultimately evolved into the X and Y chromosomes through (i) the incorporation of genes controlling sex determination and (ii) the acquisition of mechanisms to prevent recombination between the X and Y chromosomes and compensate for the difference in gene dosage of the X chromosome–encoded genes between male and female 12–17 . Thus, unlike other chromosomes, modern-day Y chromosomes have undergone numerous structural changes without correction through recombinatorial processes 17–21 . We have reported previously that chimpanzee BAC clones mapped poorly onto the human Y chromosome compared with other chromosomes 4 . Thus, we produced a high-quality sequence of the Y chromosome for the same male chimpanzee that we had previously analyzed for the chimpanzee chromosome 22 (PTR22; ref. 10). In this study, we sequenced approximately 12.7 Mb of PTRY, which corre- sponds mostly to the X-degenerate region of HSAY and partly to the chimpanzee ampliconic region (Fig. 1). Precise alignments produced from the PTRY sequences and the corresponding sequences of HSAY allowed us to carry out comparative analyses with HSAY 19 , HSAX 20 and the only other finished human-chimpanzee chromosome com- plement of HSA21 and PTR22 (ref. 10). RESULTS Analysis of the PTRY sequence We isolated clones from the whole-genome BAC library and Y-specific BAC and fosmid libraries originating from a single male chimpanzee (named Gon) that we had previously analyzed for PTR22 (ref. 10). The minimum tiling path, at the time of data freeze for this analysis, consisted of 96 minimally overlapping clones forming four clone contigs covering 905,338 bp of PTRYp and 10,074,253 bp of PTRYq, including 271 kb of the Y-specific pseudoautosomal region 1 (PAR1) sequence at the end of PTRYq (Figs. 1 and 2, Table 1, Supplementary Table 1 and Supplementary Methods online). The accuracy of the Received 18 July 2005; accepted 30 November 2005; published online 1 January 2006; corrected after print 29 January 2006 (details online); doi:10.1038/ng1729 1 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 H.-S.P. (hspark@kribb.re.kr) or A.F. (afujiyam@nii.ac.jp). 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