Systematic identification and characterization of repeat sequences in African swine fever virus genomes
Abstract African swine fever virus (ASFV) is a large DNA virus that infects domestic pigs with high morbidity and mortality rates. Repeat sequences, which are DNA sequence elements that are repeated more than twice in the genome, play an important role in the ASFV genome. The majority of repeat sequ...
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| Format: | Article |
| Language: | English |
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BMC
2022-12-01
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| Series: | Veterinary Research |
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| Online Access: | https://doi.org/10.1186/s13567-022-01119-9 |
| _version_ | 1811190328582995968 |
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| author | Zhaozhong Zhu Shengqiang Ge Zena Cai Yifan Wu Congyu Lu Zheng Zhang Ping Fu Longfei Mao Xiaodong Wu Yousong Peng |
| author_facet | Zhaozhong Zhu Shengqiang Ge Zena Cai Yifan Wu Congyu Lu Zheng Zhang Ping Fu Longfei Mao Xiaodong Wu Yousong Peng |
| author_sort | Zhaozhong Zhu |
| collection | DOAJ |
| description | Abstract African swine fever virus (ASFV) is a large DNA virus that infects domestic pigs with high morbidity and mortality rates. Repeat sequences, which are DNA sequence elements that are repeated more than twice in the genome, play an important role in the ASFV genome. The majority of repeat sequences, however, have not been identified and characterized in a systematic manner. In this study, three types of repeat sequences, including microsatellites, minisatellites and short interspersed nuclear elements (SINEs), were identified in the ASFV genome, and their distribution, structure, function, and evolutionary history were investigated. Most repeat sequences were observed in noncoding regions and at the 5’ end of the genome. Noncoding repeat sequences tended to form enhancers, whereas coding repeat sequences had a lower ratio of alpha-helix and beta-sheet and a higher ratio of loop structure and surface amino acids than nonrepeat sequences. In addition, the repeat sequences tended to encode penetrating and antimicrobial peptides. Further analysis of the evolution of repeat sequences revealed that the pan-repeat sequences presented an open state, showing the diversity of repeat sequences. Finally, CpG islands were observed to be negatively correlated with repeat sequence occurrences, suggesting that they may affect the generation of repeat sequences. Overall, this study emphasizes the importance of repeat sequences in ASFVs, and these results can aid in understanding the virus's function and evolution. |
| first_indexed | 2024-04-11T14:48:23Z |
| format | Article |
| id | doaj.art-a7c17599dd144248b49776601ffe9af7 |
| institution | Directory Open Access Journal |
| issn | 1297-9716 |
| language | English |
| last_indexed | 2024-04-11T14:48:23Z |
| publishDate | 2022-12-01 |
| publisher | BMC |
| record_format | Article |
| series | Veterinary Research |
| spelling | doaj.art-a7c17599dd144248b49776601ffe9af72022-12-22T04:17:33ZengBMCVeterinary Research1297-97162022-12-0153111110.1186/s13567-022-01119-9Systematic identification and characterization of repeat sequences in African swine fever virus genomesZhaozhong Zhu0Shengqiang Ge1Zena Cai2Yifan Wu3Congyu Lu4Zheng Zhang5Ping Fu6Longfei Mao7Xiaodong Wu8Yousong Peng9Bioinformatics Center, College of Biology, Hunan Provincial Key Laboratory of Medical Virology, Hunan UniversityChina Animal Health and Epidemiology CenterBioinformatics Center, College of Biology, Hunan Provincial Key Laboratory of Medical Virology, Hunan UniversityBioinformatics Center, College of Biology, Hunan Provincial Key Laboratory of Medical Virology, Hunan UniversityBioinformatics Center, College of Biology, Hunan Provincial Key Laboratory of Medical Virology, Hunan UniversityBioinformatics Center, College of Biology, Hunan Provincial Key Laboratory of Medical Virology, Hunan UniversityBioinformatics Center, College of Biology, Hunan Provincial Key Laboratory of Medical Virology, Hunan UniversityBioinformatics Center, College of Biology, Hunan Provincial Key Laboratory of Medical Virology, Hunan UniversityChina Animal Health and Epidemiology CenterBioinformatics Center, College of Biology, Hunan Provincial Key Laboratory of Medical Virology, Hunan UniversityAbstract African swine fever virus (ASFV) is a large DNA virus that infects domestic pigs with high morbidity and mortality rates. Repeat sequences, which are DNA sequence elements that are repeated more than twice in the genome, play an important role in the ASFV genome. The majority of repeat sequences, however, have not been identified and characterized in a systematic manner. In this study, three types of repeat sequences, including microsatellites, minisatellites and short interspersed nuclear elements (SINEs), were identified in the ASFV genome, and their distribution, structure, function, and evolutionary history were investigated. Most repeat sequences were observed in noncoding regions and at the 5’ end of the genome. Noncoding repeat sequences tended to form enhancers, whereas coding repeat sequences had a lower ratio of alpha-helix and beta-sheet and a higher ratio of loop structure and surface amino acids than nonrepeat sequences. In addition, the repeat sequences tended to encode penetrating and antimicrobial peptides. Further analysis of the evolution of repeat sequences revealed that the pan-repeat sequences presented an open state, showing the diversity of repeat sequences. Finally, CpG islands were observed to be negatively correlated with repeat sequence occurrences, suggesting that they may affect the generation of repeat sequences. Overall, this study emphasizes the importance of repeat sequences in ASFVs, and these results can aid in understanding the virus's function and evolution.https://doi.org/10.1186/s13567-022-01119-9ASFVrepeat sequencesevolutiongenetic diversity |
| spellingShingle | Zhaozhong Zhu Shengqiang Ge Zena Cai Yifan Wu Congyu Lu Zheng Zhang Ping Fu Longfei Mao Xiaodong Wu Yousong Peng Systematic identification and characterization of repeat sequences in African swine fever virus genomes Veterinary Research ASFV repeat sequences evolution genetic diversity |
| title | Systematic identification and characterization of repeat sequences in African swine fever virus genomes |
| title_full | Systematic identification and characterization of repeat sequences in African swine fever virus genomes |
| title_fullStr | Systematic identification and characterization of repeat sequences in African swine fever virus genomes |
| title_full_unstemmed | Systematic identification and characterization of repeat sequences in African swine fever virus genomes |
| title_short | Systematic identification and characterization of repeat sequences in African swine fever virus genomes |
| title_sort | systematic identification and characterization of repeat sequences in african swine fever virus genomes |
| topic | ASFV repeat sequences evolution genetic diversity |
| url | https://doi.org/10.1186/s13567-022-01119-9 |
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