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Yang L, Malhotra R, Chikhi R, Elleder D, Kaiser T, Rong J, Medvedev P, Poss M. Recombination marks the evolutionary dynamics of a recently endogenized retrovirus. Mol Biol Evol 2021; 38:5423-5436. [PMID: 34480565 PMCID: PMC8662619 DOI: 10.1093/molbev/msab252] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
All vertebrate genomes have been colonized by retroviruses along their evolutionary trajectory. Although endogenous retroviruses (ERVs) can contribute important physiological functions to contemporary hosts, such benefits are attributed to long-term coevolution of ERV and host because germline infections are rare and expansion is slow, and because the host effectively silences them. The genomes of several outbred species including mule deer (Odocoileus hemionus) are currently being colonized by ERVs, which provides an opportunity to study ERV dynamics at a time when few are fixed. We previously established the locus-specific distribution of cervid ERV (CrERV) in populations of mule deer. In this study, we determine the molecular evolutionary processes acting on CrERV at each locus in the context of phylogenetic origin, genome location, and population prevalence. A mule deer genome was de novo assembled from short- and long-insert mate pair reads and CrERV sequence generated at each locus. We report that CrERV composition and diversity have recently measurably increased by horizontal acquisition of a new retrovirus lineage. This new lineage has further expanded CrERV burden and CrERV genomic diversity by activating and recombining with existing CrERV. Resulting interlineage recombinants then endogenize and subsequently expand. CrERV loci are significantly closer to genes than expected if integration were random and gene proximity might explain the recent expansion of one recombinant CrERV lineage. Thus, in mule deer, retroviral colonization is a dynamic period in the molecular evolution of CrERV that also provides a burst of genomic diversity to the host population.
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Affiliation(s)
- Lei Yang
- Department of Biology, The Pennsylvania State University, University Park, PA, 16802, USA.,Center for Comparative Genomics and Bioinformatics, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Raunaq Malhotra
- Department of Computer Science and Engineering, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Rayan Chikhi
- Center for Comparative Genomics and Bioinformatics, The Pennsylvania State University, University Park, PA, 16802, USA.,Department of Computer Science and Engineering, The Pennsylvania State University, University Park, PA, 16802, USA.,Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Daniel Elleder
- Department of Biology, The Pennsylvania State University, University Park, PA, 16802, USA.,Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, 1083, 14220, Czech Republic Vídeňská Prague
| | - Theodora Kaiser
- Department of Biology, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Jesse Rong
- Department of Computer Science and Engineering, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Paul Medvedev
- Center for Comparative Genomics and Bioinformatics, The Pennsylvania State University, University Park, PA, 16802, USA.,Department of Computer Science and Engineering, The Pennsylvania State University, University Park, PA, 16802, USA.,Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Mary Poss
- Department of Biology, The Pennsylvania State University, University Park, PA, 16802, USA.,Center for Comparative Genomics and Bioinformatics, The Pennsylvania State University, University Park, PA, 16802, USA
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Hron T, Fabryova H, Elleder D. Insight into the epigenetic landscape of a currently endogenizing gammaretrovirus in mule deer (Odocoileus hemionus). Genomics 2019; 112:886-896. [PMID: 31175981 DOI: 10.1016/j.ygeno.2019.06.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Revised: 04/26/2019] [Accepted: 06/03/2019] [Indexed: 01/22/2023]
Abstract
Endogenous retroviruses (ERVs) constitute a significant part of vertebrate genomes. They originated from past retroviral infections and some of them retain transcriptional activity. The key mechanism avoiding uncontrolled ERV transcription is DNA methylation-mediated epigenetic silencing. Despite numerous studies describing the involvement of ERV activity in cellular processes, epigenetic regulation of ERVs is still poorly understood. We previously described a cervid endogenous retrovirus (CrERV) in the mule deer genome. This virus exhibits massive insertional polymorphism, suggesting recent activity. Here we employed NGS-based strategy to determine the methylation pattern of CrERV integrations in four mule deer. Besides the vast majority of methylated integrations, we identified a tiny fraction of demethylated proviral copies. These copies represent evolutionary older integrations located near gene promoters. In general, our work is a first attempt to characterize the epigenetic landscape of insertionally polymorphic ERV on a whole-genome scale and offers insight into its interactions with a host.
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Affiliation(s)
- Tomas Hron
- Institute of Molecular Genetics, The Czech Academy of Sciences, Videnska 1083, Prague, 14220, Czech Republic; Faculty of Science, Charles University, Albertov 6, 128 43 Praha 2, Czech Republic.
| | - Helena Fabryova
- Institute of Molecular Genetics, The Czech Academy of Sciences, Videnska 1083, Prague, 14220, Czech Republic; Faculty of Science, Charles University, Albertov 6, 128 43 Praha 2, Czech Republic
| | - Daniel Elleder
- Institute of Molecular Genetics, The Czech Academy of Sciences, Videnska 1083, Prague, 14220, Czech Republic.
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Fábryová H, Hron T, Kabíčková H, Poss M, Elleder D. Induction and characterization of a replication competent cervid endogenous gammaretrovirus (CrERV) from mule deer cells. Virology 2015. [PMID: 26218214 DOI: 10.1016/j.virol.2015.07.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Endogenous retroviruses (ERVs) were acquired during evolution of their host organisms after infection and mendelian inheritance in the germline by their exogenous counterparts. The ERVs can spread in the host genome and in some cases they affect the host phenotype. The cervid endogenous gammaretrovirus (CrERV) is one of only a few well-defined examples of evolutionarily recent invasion of mammalian genome by retroviruses. Thousands of insertionally polymorphic CrERV integration sites have been detected in wild ranging mule deer (Odocoileus hemionus) host populations. Here, we describe for the first time induction of replication competent CrERV by cocultivation of deer and human cells. We characterize the physical properties and tropism of the induced virus. The genomic sequence of the induced virus is phylogenetically related to the evolutionarily young endogenous CrERVs described so far. We also describe the level of replication block of CrERV on deer cells and its capacity to establish superinfection interference.
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Affiliation(s)
- Helena Fábryová
- Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, 14220 Prague, Czech Republic
| | - Tomáš Hron
- Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, 14220 Prague, Czech Republic
| | - Hana Kabíčková
- Military Health Institute, Department of Microbiology and Biological Research, 16001 Prague, Czech Republic
| | - Mary Poss
- Department of Biology, Center for Infectious Disease Dynamics, Pennsylvania State University, University Park, PA 16801, USA
| | - Daniel Elleder
- Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, 14220 Prague, Czech Republic.
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