1,2Ryuichi Sakate, 2Yoshiharu Sato, 3Akihiro Matsuya, 1,2Yasuyuki Fujii, 2,4Takeshi Itoh, 2,5Takashi Gojobori, 2Tadashi Imanishi
1Japan Biological Information Research Center, Japan Biological Informatics Consortium, Aomi 2-45, Koto-ku, Tokyo 135-0064, Japan, 2Biological Information Research Center, National Institute of Advanced Industrial Science and Technology, Aomi 2-45, Koto-ku, Tokyo 135-0064, Japan, 3Life Science Group, Hitachi, Ltd., 1-3-1 Minamidai, Kawagoe, Saitama 350-1165, Japan, 4Genome Research Department, National Institute of Agrobiological Science, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602, Japan, 5Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics, Yata 1111, Mishima, Shizuoka 411-8540, Japan
In order to elucidate the evolutionary process of human genome organization, we compared human, chimpanzee, mouse and rat genomes and built genome alignments that originated from non-repetitive sequences. Conserved repetitive sequences adjacent to non-repetitive sequences were included in the genome alignments. We detected evolutionarily conserved regions among the four species then partitioned the human genome with the patterns of conservation. We discovered that 19.9% of the human genome sequences were conserved among the four species while 43.9% of the sequences were conserved specifically between human and chimpanzee lineages. Considering about 50% of the human genome sequences consisting of repetitive sequences, it was intriguing that only 17.5% of the conserved human genome sequences among the four species consisted of repetitive sequences while 60.6% of the conserved sequences between human and chimpanzee lineages consisted of repetitive sequences. We also confirmed that genes densely locate in the conserved genome regions among the four species. The results imply that primate-specific genome regions in the human genome, which may have been obtained after the divergence of primates and rodents, are larger than expected. Additionally, it provides important clues for understanding the evolution of the human genome from the mammalian lineage.
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