Detection of non-reference porcine endogenous retrovirus loci in the Vietnamese native pig genome
Abstract The Vietnamese native pig (VnP)—a porcine breed with a small body—has proven suitable as a biomedical animal model. Here, we demonstrate that, compared to other breeds, VnPs have fewer copies of porcine endogenous retroviruses (PERVs), which pose a risk for xenotransplantation of pig organs...
| Main Authors: | , , , , , , , |
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| Format: | Article |
| Language: | English |
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Nature Portfolio
2022-06-01
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| Series: | Scientific Reports |
| Online Access: | https://doi.org/10.1038/s41598-022-14654-4 |
| _version_ | 1811227098910556160 |
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| author | Shinya Ishihara Masahiko Kumagai Aisaku Arakawa Masaaki Taniguchi Ngo Thi Kim Cuc Lan Doan Pham Satoshi Mikawa Kazuhiro Kikuchi |
| author_facet | Shinya Ishihara Masahiko Kumagai Aisaku Arakawa Masaaki Taniguchi Ngo Thi Kim Cuc Lan Doan Pham Satoshi Mikawa Kazuhiro Kikuchi |
| author_sort | Shinya Ishihara |
| collection | DOAJ |
| description | Abstract The Vietnamese native pig (VnP)—a porcine breed with a small body—has proven suitable as a biomedical animal model. Here, we demonstrate that, compared to other breeds, VnPs have fewer copies of porcine endogenous retroviruses (PERVs), which pose a risk for xenotransplantation of pig organs to humans. More specifically, we sought to characterize non-reference PERVs (nrPERVs) that were previously unidentified in the reference genome. To this end, we used whole-genome sequencing data to identify nrPERV loci with long terminal repeat (LTR) sequences in VnPs. RetroSeq was used to estimate nrPERV loci based on the most current porcine reference genome (Sscrofa11.1). LTRs were detected using de novo sequencing read assembly near the loci containing the target site duplication sequences in the inferred regions. A total of 21 non-reference LTR loci were identified and separated into two subtypes based on phylogenetic analysis. Moreover, PERVs within the detected LTR loci were identified, the presence of which was confirmed using conventional PCR and Sanger sequencing. These novel loci represent previously unknown PERVs as they have not been identified in the porcine reference genome. Thus, our RetroSeq method accurately detects novel PERV loci, and can be applied for development of a useful biomedical model. |
| first_indexed | 2024-04-12T09:35:52Z |
| format | Article |
| id | doaj.art-9fb47f4ac67b4a45b54150e083d1f733 |
| institution | Directory Open Access Journal |
| issn | 2045-2322 |
| language | English |
| last_indexed | 2024-04-12T09:35:52Z |
| publishDate | 2022-06-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Scientific Reports |
| spelling | doaj.art-9fb47f4ac67b4a45b54150e083d1f7332022-12-22T03:38:14ZengNature PortfolioScientific Reports2045-23222022-06-011211910.1038/s41598-022-14654-4Detection of non-reference porcine endogenous retrovirus loci in the Vietnamese native pig genomeShinya Ishihara0Masahiko Kumagai1Aisaku Arakawa2Masaaki Taniguchi3Ngo Thi Kim Cuc4Lan Doan Pham5Satoshi Mikawa6Kazuhiro Kikuchi7Institute of Agrobiological Sciences, National Agriculture and Food Research OrganizationAdvanced Analysis Center, National Agriculture and Food Research OrganizationInstitute of Livestock and Grassland Science, National Agriculture and Food Research OrganizationInstitute of Livestock and Grassland Science, National Agriculture and Food Research OrganizationNational Institute of Animal ScienceNational Institute of Animal ScienceInstitute of Agrobiological Sciences, National Agriculture and Food Research OrganizationInstitute of Agrobiological Sciences, National Agriculture and Food Research OrganizationAbstract The Vietnamese native pig (VnP)—a porcine breed with a small body—has proven suitable as a biomedical animal model. Here, we demonstrate that, compared to other breeds, VnPs have fewer copies of porcine endogenous retroviruses (PERVs), which pose a risk for xenotransplantation of pig organs to humans. More specifically, we sought to characterize non-reference PERVs (nrPERVs) that were previously unidentified in the reference genome. To this end, we used whole-genome sequencing data to identify nrPERV loci with long terminal repeat (LTR) sequences in VnPs. RetroSeq was used to estimate nrPERV loci based on the most current porcine reference genome (Sscrofa11.1). LTRs were detected using de novo sequencing read assembly near the loci containing the target site duplication sequences in the inferred regions. A total of 21 non-reference LTR loci were identified and separated into two subtypes based on phylogenetic analysis. Moreover, PERVs within the detected LTR loci were identified, the presence of which was confirmed using conventional PCR and Sanger sequencing. These novel loci represent previously unknown PERVs as they have not been identified in the porcine reference genome. Thus, our RetroSeq method accurately detects novel PERV loci, and can be applied for development of a useful biomedical model.https://doi.org/10.1038/s41598-022-14654-4 |
| spellingShingle | Shinya Ishihara Masahiko Kumagai Aisaku Arakawa Masaaki Taniguchi Ngo Thi Kim Cuc Lan Doan Pham Satoshi Mikawa Kazuhiro Kikuchi Detection of non-reference porcine endogenous retrovirus loci in the Vietnamese native pig genome Scientific Reports |
| title | Detection of non-reference porcine endogenous retrovirus loci in the Vietnamese native pig genome |
| title_full | Detection of non-reference porcine endogenous retrovirus loci in the Vietnamese native pig genome |
| title_fullStr | Detection of non-reference porcine endogenous retrovirus loci in the Vietnamese native pig genome |
| title_full_unstemmed | Detection of non-reference porcine endogenous retrovirus loci in the Vietnamese native pig genome |
| title_short | Detection of non-reference porcine endogenous retrovirus loci in the Vietnamese native pig genome |
| title_sort | detection of non reference porcine endogenous retrovirus loci in the vietnamese native pig genome |
| url | https://doi.org/10.1038/s41598-022-14654-4 |
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