Development of search system for genetic changes specifying hominization

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We conducted series of studies on following subjects in ape genome project Silver. (1) We compared human and ape sequences for 30 loci about 1kb each, and found that human-specific important changes (nonsynonymous changes and those in promoter regions) were 0.1%. If this value can be considered as representative for all "gene" region (ca. 4% of whole genome) responsible for amino acid codng and gene expression regulation, total number of candidate changes responsible for human uniqueness becomes 120, 000 (=0.001 x 0.04 x 3, 000, 000, 000). (2) We determined about 21kb region of HoxA cluster for chimpanzee, gorilla, and orangutan. Difference between human and chimpanzee was only 0.7% despite most of this region is intergenic. This suggests that integenic region in Hox cluster contains cnsiderable portion of gene regulatory sequences which are under selective constraint. (3) We determined mitochondrial DNA 16SrRNA sequences for several to dozens of individuals of chimpanzee, bonobo, gorilla, orangutan, and several gibbon species. In all species, nucleotide diversity was higher than that of human. (4) We developed of new softwares for comparative genomics of closely related species. Website of the Silver Project is http : //sayer.lab.nig.ac.jp/-silver/.