Comparative genomic analysis of inbred rat strains reveals the existence of ancestral polymorphisms

Hyeonjeong Kim, Minako Yoshihara, Mikita Suyama

研究成果: ジャーナルへの寄稿記事

抜粋

In an alignment of closely related genomic sequences, the existence of discordant mutation sites, which do not reflect the phylogenetic relationship of the genomes, is often observed. Although these discordant mutation sites are thought to have emerged by ancestral polymorphism or gene flow, their frequency and distribution in the genome have not yet been analyzed in detail. Using the genome sequences of all protein coding genes of 25 inbred rat strains, we analyzed the frequency and genome-wide distribution of the discordant mutation sites. From the comparison of different substrains, it was found that these loci are not substrain specific, but are common among different groups of substrains, suggesting that the discordant sites might have mainly emerged through ancestral polymorphism. It was also revealed that the discordant sites are not uniformly distributed along chromosomes, but are concentrated at certain genomic loci, such as RT1, major histocompatibility complex of rats, and olfactory receptors, indicating that genes known to be highly polymorphic tend to have more discordant sites. Our results also showed that loci with a high density of discordant sites are also rich in heterozygous variants, even though these are inbred strains.

元の言語英語
ページ(範囲)86-94
ページ数9
ジャーナルMammalian Genome
31
発行部数3-4
DOI
出版物ステータス出版済み - 4 1 2020

All Science Journal Classification (ASJC) codes

  • Genetics

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