Comprehensive genomic analysis reveals dynamic evolution of endogenous retroviruses that code for retroviral-like protein domains

Mobile DNA

Satomi Mitsuhashi¹  Tadashi Imanishi²  So Nakagawa³  Mahoko Takahashi Ueda⁴  Kirill Kryukov⁵  Hiroaki Mitsuhashi⁶ 

[1] Department of Human Genetics, Yokohama City University Graduate School of Medicine, 236-0004, Yokohama, Kanagawa, Japan;Department of Genomic Function and Diversity, Tokyo Medical and Dental University, Bunkyo-ku, 113-8510, Tokyo, Japan;Department of Molecular Life Science, Tokai University School of Medicine, 259-1193, Isehara, Kanagawa, Japan;Institute of Medical Sciences, Tokai University, 259-1193, Isehara, Kanagawa, Japan;Department of Molecular Life Science, Tokai University School of Medicine, 259-1193, Isehara, Kanagawa, Japan;Micro/Nano Technology Center, Tokai University, 259-1292, Hiratsuka, Kanagawa, Japan;Institute of Medical Sciences, Tokai University, 259-1193, Isehara, Kanagawa, Japan;Department of Molecular Life Science, Tokai University School of Medicine, 259-1193, Isehara, Kanagawa, Japan;Micro/Nano Technology Center, Tokai University, 259-1292, Hiratsuka, Kanagawa, Japan;Present address: Department of Genomic Function and Diversity, Tokyo Medical and Dental University, Bunkyo-ku, 113-8510, Tokyo, Japan;Department of Molecular Life Science, Tokai University School of Medicine, 259-1193, Isehara, Kanagawa, Japan;Present address: Department of Genomics and Evolutionary Biology, National Institute of Genetics, 411-8540, Mishima, Shizuoka, Japan;Micro/Nano Technology Center, Tokai University, 259-1292, Hiratsuka, Kanagawa, Japan;Department of Applied Biochemistry, School of Engineering, Tokai University, 259-1292, Hiratsuka, Kanagawa, Japan;

关键词: Endogenous retrovirus;    Retroviral-like protein domain;    Open reading frame;    Evolution;    Divergence pattern;    Co-option;    de novo gene;   

DOI  :  10.1186/s13100-020-00224-w

来源: Springer

【 摘 要 】

BackgroundEndogenous retroviruses (ERVs) are remnants of ancient retroviral infections of mammalian germline cells. A large proportion of ERVs lose their open reading frames (ORFs), while others retain them and become exapted by the host species. However, it remains unclear what proportion of ERVs possess ORFs (ERV-ORFs), become transcribed, and serve as candidates for co-opted genes.ResultsWe investigated characteristics of 176,401 ERV-ORFs containing retroviral-like protein domains (gag, pro, pol, and env) in 19 mammalian genomes. The fractions of ERVs possessing ORFs were overall small (~ 0.15%) although they varied depending on domain types as well as species. The observed divergence of ERV-ORF from their consensus sequences showed bimodal distributions, suggesting that a large proportion of ERV-ORFs either recently, or anciently, inserted themselves into mammalian genomes. Alternatively, very few ERVs lacking ORFs were found to exhibit similar divergence patterns. To identify candidates for ERV-derived genes, we estimated the ratio of non-synonymous to synonymous substitution rates (dN/dS) for ERV-ORFs in human and non-human mammalian pairs, and found that approximately 42% of the ERV-ORFs showed dN/dS < 1. Further, using functional genomics data including transcriptome sequencing, we determined that approximately 9.7% of these selected ERV-ORFs exhibited transcriptional potential.ConclusionsThese results suggest that purifying selection operates on a certain portion of ERV-ORFs, some of which may correspond to uncharacterized functional genes hidden within mammalian genomes. Together, our analyses suggest that more ERV-ORFs may be co-opted in a host-species specific manner than we currently know, which are likely to have contributed to mammalian evolution and diversification.

【 授权许可】

CC BY