Detection of long terminal repeat loci derived from endogenous retrovirus in junglefowl using whole-genome sequencing
Abstract Endogenous retroviruses (ERVs) are genetic elements present in the genome that retain traces of past viral infections. Characterization of ERVs can provide crucial insights into avian evolution. This study aimed to identify novel long terminal repeat (LTR) loci derived from ERVs (ERV-LTRs)...
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| Format: | Article |
| Language: | English |
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Nature Portfolio
2023-05-01
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| Series: | Scientific Reports |
| Online Access: | https://doi.org/10.1038/s41598-023-34520-1 |
| _version_ | 1797832066781413376 |
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| author | Shinya Ishihara |
| author_facet | Shinya Ishihara |
| author_sort | Shinya Ishihara |
| collection | DOAJ |
| description | Abstract Endogenous retroviruses (ERVs) are genetic elements present in the genome that retain traces of past viral infections. Characterization of ERVs can provide crucial insights into avian evolution. This study aimed to identify novel long terminal repeat (LTR) loci derived from ERVs (ERV-LTRs) absent in the reference genome using whole-genome sequencing data of red junglefowl, gray junglefowl, Ceylon junglefowl, and green junglefowl. In total, 835 ERV-LTR loci were identified across the four Gallus species. The numbers of ERV-LTRs loci detected in red junglefowl and its subspecies gray junglefowl, Ceylon junglefowl, and green junglefowl were 362, 216, 193, and 128, respectively. The phylogenetic tree was congruent with previously reported trees, suggesting the potential for inferring relationships among past junglefowl populations from the identified ERV-LTR loci. Of the detected loci, 306 ERV-LTRs were identified near or within the genes, and some were associated with cell adhesion. The detected ERV-LTR sequences were classified as endogenous avian retrovirus family, avian leukosis virus subgroup E, Ovex-1, and murine leukemia virus-related ERVs. In addition, the sequence of the EAV family was divided into four patterns by combining the U3, R, and U5 regions. These findings contribute to a more comprehensive understanding of the characteristics of junglefowl ERVs. |
| first_indexed | 2024-04-09T14:01:47Z |
| format | Article |
| id | doaj.art-09a72905df204ee2b8b1551e72e441e7 |
| institution | Directory Open Access Journal |
| issn | 2045-2322 |
| language | English |
| last_indexed | 2024-04-09T14:01:47Z |
| publishDate | 2023-05-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Scientific Reports |
| spelling | doaj.art-09a72905df204ee2b8b1551e72e441e72023-05-07T11:13:59ZengNature PortfolioScientific Reports2045-23222023-05-011311810.1038/s41598-023-34520-1Detection of long terminal repeat loci derived from endogenous retrovirus in junglefowl using whole-genome sequencingShinya Ishihara0Department of Animal Science, Nippon Veterinary and Life Science UniversityAbstract Endogenous retroviruses (ERVs) are genetic elements present in the genome that retain traces of past viral infections. Characterization of ERVs can provide crucial insights into avian evolution. This study aimed to identify novel long terminal repeat (LTR) loci derived from ERVs (ERV-LTRs) absent in the reference genome using whole-genome sequencing data of red junglefowl, gray junglefowl, Ceylon junglefowl, and green junglefowl. In total, 835 ERV-LTR loci were identified across the four Gallus species. The numbers of ERV-LTRs loci detected in red junglefowl and its subspecies gray junglefowl, Ceylon junglefowl, and green junglefowl were 362, 216, 193, and 128, respectively. The phylogenetic tree was congruent with previously reported trees, suggesting the potential for inferring relationships among past junglefowl populations from the identified ERV-LTR loci. Of the detected loci, 306 ERV-LTRs were identified near or within the genes, and some were associated with cell adhesion. The detected ERV-LTR sequences were classified as endogenous avian retrovirus family, avian leukosis virus subgroup E, Ovex-1, and murine leukemia virus-related ERVs. In addition, the sequence of the EAV family was divided into four patterns by combining the U3, R, and U5 regions. These findings contribute to a more comprehensive understanding of the characteristics of junglefowl ERVs.https://doi.org/10.1038/s41598-023-34520-1 |
| spellingShingle | Shinya Ishihara Detection of long terminal repeat loci derived from endogenous retrovirus in junglefowl using whole-genome sequencing Scientific Reports |
| title | Detection of long terminal repeat loci derived from endogenous retrovirus in junglefowl using whole-genome sequencing |
| title_full | Detection of long terminal repeat loci derived from endogenous retrovirus in junglefowl using whole-genome sequencing |
| title_fullStr | Detection of long terminal repeat loci derived from endogenous retrovirus in junglefowl using whole-genome sequencing |
| title_full_unstemmed | Detection of long terminal repeat loci derived from endogenous retrovirus in junglefowl using whole-genome sequencing |
| title_short | Detection of long terminal repeat loci derived from endogenous retrovirus in junglefowl using whole-genome sequencing |
| title_sort | detection of long terminal repeat loci derived from endogenous retrovirus in junglefowl using whole genome sequencing |
| url | https://doi.org/10.1038/s41598-023-34520-1 |
| work_keys_str_mv | AT shinyaishihara detectionoflongterminalrepeatlociderivedfromendogenousretrovirusinjunglefowlusingwholegenomesequencing |