Characteristic features of porcine endogenous retroviruses in Vietnamese native pigs
We aimed to clarify the genomic characteristics of porcine endogenous retroviruses (PERVs) in Vietnamese native pig (VnP) breeds. First, we investigated genetic polymorphisms in β‐ and γ‐like PERVs, and we then measured the copy numbers of infectious γ‐like PERVs (PERV‐A, B, and C). We purified geno...
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| Veröffentlicht in: | Animal science journal 2020-01, Vol.91 (1), p.e13336-n/a |
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| creator | Ishihara, Shinya Dang‐Nguyen, Thanh Q. Kikuchi, Kazuhiro Arakawa, Aisaku Mikawa, Satoshi Osaki, Makoto Otoi, Takeshige Luu, Quang Minh Nguyen, Thanh Son Taniguchi, Masaaki |
| description | We aimed to clarify the genomic characteristics of porcine endogenous retroviruses (PERVs) in Vietnamese native pig (VnP) breeds. First, we investigated genetic polymorphisms in β‐ and γ‐like PERVs, and we then measured the copy numbers of infectious γ‐like PERVs (PERV‐A, B, and C). We purified genomic DNA from 15 VnP breeds from 12 regions all over the country and three Western pig breeds as controls, and investigated genetic polymorphisms in all known PERVs, including the beta (β)1–4 and gamma (γ)1–5 groups. PERVs of β1, β2, β3, and γ4 were highly polymorphic with VnP‐specific haplotypes. We did not identify genetic polymorphisms in β4, γ1, or γ2 PERVs. We then applied a real‐time polymerase chain reaction–based method to estimate copy numbers of the gag, pol, and env genes of γ1 PERVs (defined as A, B, and C). VnP breeds showed significantly lower copy number of the PERV genes compared with the Western pig breeds (on average, 16.2 and 35.7 copies, respectively, p |
| doi_str_mv | 10.1111/asj.13336 |
| format | Article |
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First, we investigated genetic polymorphisms in β‐ and γ‐like PERVs, and we then measured the copy numbers of infectious γ‐like PERVs (PERV‐A, B, and C). We purified genomic DNA from 15 VnP breeds from 12 regions all over the country and three Western pig breeds as controls, and investigated genetic polymorphisms in all known PERVs, including the beta (β)1–4 and gamma (γ)1–5 groups. PERVs of β1, β2, β3, and γ4 were highly polymorphic with VnP‐specific haplotypes. We did not identify genetic polymorphisms in β4, γ1, or γ2 PERVs. We then applied a real‐time polymerase chain reaction–based method to estimate copy numbers of the gag, pol, and env genes of γ1 PERVs (defined as A, B, and C). VnP breeds showed significantly lower copy number of the PERV genes compared with the Western pig breeds (on average, 16.2 and 35.7 copies, respectively, p < .05). Two VnP breeds showed significantly higher copy number compared with the other VnPs (p < .05). Our results elucidated that VnPs have specific haplotypes and a low copy number of PERV genes.</description><identifier>ISSN: 1344-3941</identifier><identifier>EISSN: 1740-0929</identifier><identifier>DOI: 10.1111/asj.13336</identifier><identifier>PMID: 32219916</identifier><language>eng</language><publisher>Australia: Blackwell Publishing Ltd</publisher><subject>Animals ; Copy number ; copy number variation ; Deoxyribonucleic acid ; DNA ; Endogenous retroviruses ; Gene Dosage ; Gene polymorphism ; Genes ; Genome, Viral - genetics ; haplotype analysis ; Haplotypes ; native pigs ; Polymerase chain reaction ; Polymorphism, Genetic ; porcine endogenous retrovirus ; Retroviridae - genetics ; Swine ; Swine - virology ; Vietnam ; Xenotransplantation</subject><ispartof>Animal science journal, 2020-01, Vol.91 (1), p.e13336-n/a</ispartof><rights>2020 Japanese Society of Animal Science</rights><rights>2020 Japanese Society of Animal Science.</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c4216-b06ebc3f0a3a31aadac7d3ac7a20fa74fd407e25f8fa25a9290eea9a5821acaf3</citedby><cites>FETCH-LOGICAL-c4216-b06ebc3f0a3a31aadac7d3ac7a20fa74fd407e25f8fa25a9290eea9a5821acaf3</cites><orcidid>0000-0002-7198-9237 ; 0000-0001-8194-3577 ; 0000-0001-8176-4827</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://onlinelibrary.wiley.com/doi/pdf/10.1111%2Fasj.13336$$EPDF$$P50$$Gwiley$$H</linktopdf><linktohtml>$$Uhttps://onlinelibrary.wiley.com/doi/full/10.1111%2Fasj.13336$$EHTML$$P50$$Gwiley$$H</linktohtml><link.rule.ids>314,776,780,1411,27901,27902,45550,45551</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/32219916$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Ishihara, Shinya</creatorcontrib><creatorcontrib>Dang‐Nguyen, Thanh Q.</creatorcontrib><creatorcontrib>Kikuchi, Kazuhiro</creatorcontrib><creatorcontrib>Arakawa, Aisaku</creatorcontrib><creatorcontrib>Mikawa, Satoshi</creatorcontrib><creatorcontrib>Osaki, Makoto</creatorcontrib><creatorcontrib>Otoi, Takeshige</creatorcontrib><creatorcontrib>Luu, Quang Minh</creatorcontrib><creatorcontrib>Nguyen, Thanh Son</creatorcontrib><creatorcontrib>Taniguchi, Masaaki</creatorcontrib><title>Characteristic features of porcine endogenous retroviruses in Vietnamese native pigs</title><title>Animal science journal</title><addtitle>Anim Sci J</addtitle><description>We aimed to clarify the genomic characteristics of porcine endogenous retroviruses (PERVs) in Vietnamese native pig (VnP) breeds. First, we investigated genetic polymorphisms in β‐ and γ‐like PERVs, and we then measured the copy numbers of infectious γ‐like PERVs (PERV‐A, B, and C). We purified genomic DNA from 15 VnP breeds from 12 regions all over the country and three Western pig breeds as controls, and investigated genetic polymorphisms in all known PERVs, including the beta (β)1–4 and gamma (γ)1–5 groups. PERVs of β1, β2, β3, and γ4 were highly polymorphic with VnP‐specific haplotypes. We did not identify genetic polymorphisms in β4, γ1, or γ2 PERVs. We then applied a real‐time polymerase chain reaction–based method to estimate copy numbers of the gag, pol, and env genes of γ1 PERVs (defined as A, B, and C). VnP breeds showed significantly lower copy number of the PERV genes compared with the Western pig breeds (on average, 16.2 and 35.7 copies, respectively, p < .05). Two VnP breeds showed significantly higher copy number compared with the other VnPs (p < .05). Our results elucidated that VnPs have specific haplotypes and a low copy number of PERV genes.</description><subject>Animals</subject><subject>Copy number</subject><subject>copy number variation</subject><subject>Deoxyribonucleic acid</subject><subject>DNA</subject><subject>Endogenous retroviruses</subject><subject>Gene Dosage</subject><subject>Gene polymorphism</subject><subject>Genes</subject><subject>Genome, Viral - genetics</subject><subject>haplotype analysis</subject><subject>Haplotypes</subject><subject>native pigs</subject><subject>Polymerase chain reaction</subject><subject>Polymorphism, Genetic</subject><subject>porcine endogenous retrovirus</subject><subject>Retroviridae - genetics</subject><subject>Swine</subject><subject>Swine - virology</subject><subject>Vietnam</subject><subject>Xenotransplantation</subject><issn>1344-3941</issn><issn>1740-0929</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2020</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNp1kE1PwzAMhiMEYmNw4A-gSlzg0C1fbdfjNPEpJA4MrpGXOiNT146kHdq_J6ODAxI-2Jb86LX9EnLO6JCFGIFfDpkQIj0gfZZJGtOc54ehF1LGIpesR068X1LKspwmx6QnOGd5ztI-mU3fwYFu0FnfWB0ZhKZ16KPaROvaaVthhFVRL7CqWx85bFy9sa71AbFV9GaxqWCFHqMKGrvBaG0X_pQcGSg9nu3rgLze3sym9_HT893DdPIUa8lZGs9pinMtDAUBggEUoLNChAScGsikKSTNkCdmbIAnEH6iiJBDMuYMNBgxIFed7trVHy36Rq2s11iWUGG4VnExDotkkomAXv5Bl3XrqnCd4jLMszFNdtR1R2lXe-_QqLWzK3BbxajaWa2C1erb6sBe7BXb-QqLX_LH2wCMOuDTlrj9X0lNXh47yS_g4omO</recordid><startdate>202001</startdate><enddate>202001</enddate><creator>Ishihara, Shinya</creator><creator>Dang‐Nguyen, Thanh Q.</creator><creator>Kikuchi, Kazuhiro</creator><creator>Arakawa, Aisaku</creator><creator>Mikawa, Satoshi</creator><creator>Osaki, Makoto</creator><creator>Otoi, Takeshige</creator><creator>Luu, Quang Minh</creator><creator>Nguyen, Thanh Son</creator><creator>Taniguchi, Masaaki</creator><general>Blackwell Publishing Ltd</general><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>7QL</scope><scope>7T7</scope><scope>7TK</scope><scope>7U9</scope><scope>8FD</scope><scope>C1K</scope><scope>FR3</scope><scope>H94</scope><scope>M7N</scope><scope>P64</scope><scope>RC3</scope><scope>7X8</scope><orcidid>https://orcid.org/0000-0002-7198-9237</orcidid><orcidid>https://orcid.org/0000-0001-8194-3577</orcidid><orcidid>https://orcid.org/0000-0001-8176-4827</orcidid></search><sort><creationdate>202001</creationdate><title>Characteristic features of porcine endogenous retroviruses in Vietnamese native pigs</title><author>Ishihara, Shinya ; Dang‐Nguyen, Thanh Q. ; Kikuchi, Kazuhiro ; Arakawa, Aisaku ; Mikawa, Satoshi ; Osaki, Makoto ; Otoi, Takeshige ; Luu, Quang Minh ; Nguyen, Thanh Son ; Taniguchi, Masaaki</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c4216-b06ebc3f0a3a31aadac7d3ac7a20fa74fd407e25f8fa25a9290eea9a5821acaf3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2020</creationdate><topic>Animals</topic><topic>Copy number</topic><topic>copy number variation</topic><topic>Deoxyribonucleic acid</topic><topic>DNA</topic><topic>Endogenous retroviruses</topic><topic>Gene Dosage</topic><topic>Gene polymorphism</topic><topic>Genes</topic><topic>Genome, Viral - genetics</topic><topic>haplotype analysis</topic><topic>Haplotypes</topic><topic>native pigs</topic><topic>Polymerase chain reaction</topic><topic>Polymorphism, Genetic</topic><topic>porcine endogenous retrovirus</topic><topic>Retroviridae - genetics</topic><topic>Swine</topic><topic>Swine - virology</topic><topic>Vietnam</topic><topic>Xenotransplantation</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Ishihara, Shinya</creatorcontrib><creatorcontrib>Dang‐Nguyen, Thanh Q.</creatorcontrib><creatorcontrib>Kikuchi, Kazuhiro</creatorcontrib><creatorcontrib>Arakawa, Aisaku</creatorcontrib><creatorcontrib>Mikawa, Satoshi</creatorcontrib><creatorcontrib>Osaki, Makoto</creatorcontrib><creatorcontrib>Otoi, Takeshige</creatorcontrib><creatorcontrib>Luu, Quang Minh</creatorcontrib><creatorcontrib>Nguyen, Thanh Son</creatorcontrib><creatorcontrib>Taniguchi, Masaaki</creatorcontrib><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>Bacteriology Abstracts (Microbiology B)</collection><collection>Industrial and Applied Microbiology Abstracts (Microbiology A)</collection><collection>Neurosciences Abstracts</collection><collection>Virology and AIDS Abstracts</collection><collection>Technology Research Database</collection><collection>Environmental Sciences and Pollution Management</collection><collection>Engineering Research Database</collection><collection>AIDS and Cancer Research Abstracts</collection><collection>Algology Mycology and Protozoology Abstracts (Microbiology C)</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>Genetics Abstracts</collection><collection>MEDLINE - Academic</collection><jtitle>Animal science journal</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Ishihara, Shinya</au><au>Dang‐Nguyen, Thanh Q.</au><au>Kikuchi, Kazuhiro</au><au>Arakawa, Aisaku</au><au>Mikawa, Satoshi</au><au>Osaki, Makoto</au><au>Otoi, Takeshige</au><au>Luu, Quang Minh</au><au>Nguyen, Thanh Son</au><au>Taniguchi, Masaaki</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Characteristic features of porcine endogenous retroviruses in Vietnamese native pigs</atitle><jtitle>Animal science journal</jtitle><addtitle>Anim Sci J</addtitle><date>2020-01</date><risdate>2020</risdate><volume>91</volume><issue>1</issue><spage>e13336</spage><epage>n/a</epage><pages>e13336-n/a</pages><issn>1344-3941</issn><eissn>1740-0929</eissn><abstract>We aimed to clarify the genomic characteristics of porcine endogenous retroviruses (PERVs) in Vietnamese native pig (VnP) breeds. First, we investigated genetic polymorphisms in β‐ and γ‐like PERVs, and we then measured the copy numbers of infectious γ‐like PERVs (PERV‐A, B, and C). We purified genomic DNA from 15 VnP breeds from 12 regions all over the country and three Western pig breeds as controls, and investigated genetic polymorphisms in all known PERVs, including the beta (β)1–4 and gamma (γ)1–5 groups. PERVs of β1, β2, β3, and γ4 were highly polymorphic with VnP‐specific haplotypes. We did not identify genetic polymorphisms in β4, γ1, or γ2 PERVs. We then applied a real‐time polymerase chain reaction–based method to estimate copy numbers of the gag, pol, and env genes of γ1 PERVs (defined as A, B, and C). VnP breeds showed significantly lower copy number of the PERV genes compared with the Western pig breeds (on average, 16.2 and 35.7 copies, respectively, p < .05). Two VnP breeds showed significantly higher copy number compared with the other VnPs (p < .05). Our results elucidated that VnPs have specific haplotypes and a low copy number of PERV genes.</abstract><cop>Australia</cop><pub>Blackwell Publishing Ltd</pub><pmid>32219916</pmid><doi>10.1111/asj.13336</doi><tpages>8</tpages><orcidid>https://orcid.org/0000-0002-7198-9237</orcidid><orcidid>https://orcid.org/0000-0001-8194-3577</orcidid><orcidid>https://orcid.org/0000-0001-8176-4827</orcidid></addata></record> |
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| subjects | Animals Copy number copy number variation Deoxyribonucleic acid DNA Endogenous retroviruses Gene Dosage Gene polymorphism Genes Genome, Viral - genetics haplotype analysis Haplotypes native pigs Polymerase chain reaction Polymorphism, Genetic porcine endogenous retrovirus Retroviridae - genetics Swine Swine - virology Vietnam Xenotransplantation |
| title | Characteristic features of porcine endogenous retroviruses in Vietnamese native pigs |
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