| Autor: |
Cai Chen, Zhanyu Du, Yao Zheng, Hong Chen, Ahmed A. Saleh, Naisu Yang, Mengli Wang, Phiri Azele, Xiaoyan Wang, Chengyi Song |
| Jazyk: |
angličtina |
| Rok vydání: |
2024 |
| Předmět: |
|
| Zdroj: |
Viruses, Vol 16, Iss 11, p 1801 (2024) |
| Druh dokumentu: |
article |
| ISSN: |
1999-4915 |
| DOI: |
10.3390/v16111801 |
| Popis: |
Homologous recombination events take place between the 5′ and 3′ long terminal repeats (LTRs) of ERVs, resulting in the generation of solo-LTR, which can cause solo-LTR-associated polymorphism across different genomes. In the current study, specific criteria were established for the filtration of solo-LTRs, resulting in an average of 5630 solo-LTRs being identified in 21 genomes. Subsequently, a protocol was developed for detecting solo-LTR polymorphisms in the pig genomes, resulting in the discovery of 927 predicted solo-LTR polymorphic sites. Following verification and filtration processes, 603 highly reliable solo-LTR polymorphic sites were retained, involving 446 solo-LTR presence sites (solo-LTR+) and 157 solo-LTR absence sites (solo-LTR−) relative to the reference genome. Intersection analysis with gene/functional regions revealed that 248 solo-LTR− sites and 23 solo-LTR+ sites overlapped with genes or were in the vicinity of genes or functional regions, impacting a diverse range of gene structures. Moreover, through the utilization of 156 solo-LTR polymorphic sites for population genetic analysis, it was observed that these solo-LTR loci effectively clustered various breeds together, aligning with expectations and underscoring their practical utility. This study successfully established a methodology for detecting solo-LTR polymorphic sites. By applying these methods, a total of 603 high-reliability solo-LTR polymorphic sites were pinpointed, with nearly half of them being linked to genes or functional regions. |
| Databáze: |
Directory of Open Access Journals |
| Externí odkaz: |
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