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

被引:20
|
作者
Ueda, Mahoko Takahashi [1 ,2 ,3 ]
Kryukov, Kirill [1 ,4 ]
Mitsuhashi, Satomi [5 ]
Mitsuhashi, Hiroaki [2 ,3 ,6 ]
Imanishi, Tadashi [1 ,7 ]
Nakagawa, So [1 ,2 ,7 ]
机构
[1] Tokai Univ, Sch Med, Dept Mol Life Sci, Isehara, Kanagawa 2591193, Japan
[2] Tokai Univ, Micro Nano Technol Ctr, Hiratsuka, Kanagawa 2591292, Japan
[3] Tokyo Med & Dent Univ, Dept Genom Funct & Divers, Bunkyo Ku, Tokyo 1138510, Japan
[4] Natl Inst Genet, Dept Genom & Evolutionary Biol, Mishima, Shizuoka 4118540, Japan
[5] Yokohama City Univ, Grad Sch Med, Dept Human Genet, Yokohama, Kanagawa 2360004, Japan
[6] Tokai Univ, Sch Engn, Dept Appl Biochem, Hiratsuka, Kanagawa 2591292, Japan
[7] Tokai Univ, Inst Med Sci, Isehara, Kanagawa 2591193, Japan
关键词
Endogenous retrovirus; Retroviral-like protein domain; Open reading frame; Evolution; Divergence pattern; Co-option; de novo gene; TRANSPOSABLE ELEMENTS; GAG PROTEIN; SYNCYTINS; SEQUENCE; RNA; RETROTRANSPOSON; IDENTIFICATION; TRANSCRIPTOME; PLACENTA; DATABASE;
D O I
10.1186/s13100-020-00224-w
中图分类号
Q3 [遗传学];
学科分类号
071007 ; 090102 ;
摘要
Background: Endogenous 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. Results: We investigated characteristics of 176,401 ERV-ORFs containing retroviral-like protein domains (gag,pro,pol, andenv) in 19 mammalian genomes. The fractions of ERVs possessing ORFs were overall small (similar to 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 showeddN/dS < 1. Further, using functional genomics data including transcriptome sequencing, we determined that approximately 9.7% of these selected ERV-ORFs exhibited transcriptional potential. Conclusions:These 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.
引用
收藏
页数:17
相关论文
共 20 条
  • [1] Comprehensive genomic analysis reveals dynamic evolution of endogenous retroviruses that code for retroviral-like protein domains
    Mahoko Takahashi Ueda
    Kirill Kryukov
    Satomi Mitsuhashi
    Hiroaki Mitsuhashi
    Tadashi Imanishi
    So Nakagawa
    [J]. Mobile DNA, 11
  • [2] Genomic analysis of Caenorhabditis elegans reveals ancient families of retroviral-like elements
    Bowen, NJ
    McDonald, JF
    [J]. GENOME RESEARCH, 1999, 9 (10) : 924 - 935
  • [3] Comprehensive phylogenomic analysis reveals a novel cluster of simian endogenous retroviral sequences in Colobinae monkeys
    Ikeda, Masaki
    Satomura, Kazuhiro
    Sekizuka, Tsuyoshi
    Hanada, Kentaro
    Endo, Toshinori
    Osada, Naoki
    [J]. AMERICAN JOURNAL OF PRIMATOLOGY, 2018, 80 (07)
  • [4] Functional analysis of Rossmann-like domains reveals convergent evolution of topology and reaction pathways
    Medvedev, Kirill E.
    Kinch, Lisa N.
    Schaeffer, R. Dustin
    Grishin, Nick V.
    [J]. PLOS COMPUTATIONAL BIOLOGY, 2019, 15 (12)
  • [5] Comprehensive genomic analysis reveals clonal origin and subtype-specific evolution in a case of sporadic multiple meningiomas
    Sakaguchi, Maki
    Horie, Masafumi
    Ito, Yukinobu
    Tanaka, Shingo
    Mizuguchi, Keishi
    Ikeda, Hiroko
    Kiyokawa, Etsuko
    Nakada, Mitsutoshi
    Maeda, Daichi
    [J]. BRAIN TUMOR PATHOLOGY, 2024,
  • [6] Protein Domain Analysis of Genomic Sequence Data Reveals Regulation of LRR Related Domains in Plant Transpiration in Ficus
    Lang, Tiange
    Yin, Kangquan
    Liu, Jinyu
    Cao, Kunfang
    Cannon, Charles H.
    Du, Fang K.
    [J]. PLOS ONE, 2014, 9 (09):
  • [7] Phylogenetic analysis reveals dynamic evolution of the poly(A)-binding protein gene family in plants
    Daniel R Gallie
    Renyi Liu
    [J]. BMC Evolutionary Biology, 14
  • [8] Phylogenetic analysis reveals dynamic evolution of the poly(A)-binding protein gene family in plants
    Gallie, Daniel R.
    Liu, Renyi
    [J]. BMC EVOLUTIONARY BIOLOGY, 2014, 14
  • [9] Proteomic Analysis of Ovarian Cancer Cells Reveals Dynamic Processes of Protein Secretion and Shedding of Extra-Cellular Domains
    Faca, Vitor M.
    Ventura, Aviva P.
    Fitzgibbon, Mathew P.
    Pereira-Faca, Sandra R.
    Pitteri, Sharon J.
    Green, Ann E.
    Ireton, Renee C.
    Zhang, Qing
    Wang, Hong
    O'Briant, Kathy C.
    Drescher, Charles W.
    Schummer, Michel
    McIntosh, Martin W.
    Knudsen, Beatrice S.
    Hanash, Samir M.
    [J]. PLOS ONE, 2008, 3 (06):
  • [10] Identification, Genomic Organization, and Comprehensive Expression Analysis Reveals the Implication of Cicer arietinum SKP1-like Genes in Abiotic Stress
    Varshney, Vishal
    Hazra, Abhijit
    Majee, Manoj
    [J]. JOURNAL OF PLANT GROWTH REGULATION, 2023, 42 (10) : 6074 - 6090