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

doi:10.1038/ng1729

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 journal › Article › peer-review

98 Citations (Scopus)

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.

Original language	English
Pages (from-to)	1-10
Number of pages	10
Journal	Nature Genetics
Volume	38
Issue number	2
DOIs	https://doi.org/10.1038/ng1729
Publication status	Published - 2006
Externally published	Yes

ASJC Scopus subject areas

Genetics

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Kuroki, Y., Toyoda, A., Noguchi, H., Taylor, T. D., Itoh, T., Kim, D. S., Kim, D. W., Choi, S. H., Kim, I. C., Choi, H. H., Kim, Y. S., Satta, Y., Saitou, N., Yamada, T., Morishita, S., Hattori, M., Sakaki, Y., Park, H. S., & Fujiyama, A. (2006). Comparative analysis of chimpanzee and human y chromosomes unveils complex evolutionary pathway. Nature Genetics, 38(2), 1-10. https://doi.org/10.1038/ng1729

Kuroki, Y, Toyoda, A, Noguchi, H, Taylor, TD, Itoh, T, Kim, DS, Kim, DW, Choi, SH, Kim, IC, Choi, HH, Kim, YS, Satta, Y, Saitou, N, Yamada, T, Morishita, S, Hattori, M, Sakaki, Y, Park, HS & Fujiyama, A 2006, 'Comparative analysis of chimpanzee and human y chromosomes unveils complex evolutionary pathway', Nature Genetics, vol. 38, no. 2, pp. 1-10. https://doi.org/10.1038/ng1729

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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.",

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AU - Kim, Dae Won

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AU - Satta, Yoko

AU - Saitou, Naruya

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AU - Morishita, Shinichi

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AU - Park, Hong Seog

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

Abstract

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