International Mammalian Genome Society

The 14th International Mouse Genome Conference (2000)

C11. Comparative Genomics of Mouse ESTs with particular reference to Evolution of Mammalian Genomes.

Atsushi Ogura, Tadashi Imanishi, Kazuho Ikeo, and Takashi Gojobori
Center for Information Biology, Natl. Inst. Genet., Mishima 411-8540, JAPAN

The genome sequencing of over 30 different species has been completed so far, and the genome projects of more than 200 other species are now in progress. Moreover, many EST (Expressed Sequenced Tag) projects have been also conducted. The sequence data that are increasingly produced from those projects give us a unique opportunity for elucidating gene interaction and genetic network by comparing the sequence data between different species of interest. In this study, we used human and mouse sequence data for comparative genomics, because a hypothesis derived from comparative genomics may be easily confirmed in the laboratory in the mouse. With the aim of identifying orthologous gene pairs between human and mouse genomes and understanding evolutionary importance of the alternative splicing mechanism, we compared sequence data among mouse ESTs, human ESTs, and the human genome. First, we have located equivalent position of each mouse EST in the human genome sequence, taking into account the fact that the sequence homology of genes between mouse and human is, on average, about 80%. We then examined the homologous genes between the two species. In practice, for the human genome, we used assembled human genomic sequences from DDBJ/CIB Human Genomics Studio ( For mouse ESTs, we used 910,000 mouse full-length cDNA 3'-end sequences (redundant) and 120,000 mouse full-length cDNA 3'-end sequences (non-redundant, with poly-A site removed) from Riken Mouse Encyclopedia Index Archive ( As a result, we found homologous relationships between human and mouse genes. Examining the homologous genes in more detail, we found three kinds of gene groups. The first group is mouse ESTs each of which correspond to a single human gene, implying that these genes may be orthologous genes. This implication is also supported by the whole comparison between human and mouse ESTs. The second group is mouse ESTs that correspond to different exons that are located in different positions of the human genome. This implies that the outcome of either alternative splicing or exon shuffling. The last group is mouse ESTs each of which was found in multiple positions in the human genome. This indicates that such a gene might correspond to a gene family in the human genome. We plan to use this approach to establish a model for gene interaction and genetic network in the next stage, giving us insight into evolution of mammalian genomes.

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