Hotspots of genetic change in Yersinia pestis
Abstract The relative contributions of mutation rate variation, selection, and recombination in shaping genomic variation in bacterial populations remain poorly understood. Here we analyze 3318 Yersinia pestis genomes, spanning nearly a century and including 2336 newly sequenced strains, to shed lig...
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| Format: | Article |
| Language: | English |
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Nature Portfolio
2025-01-01
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| Series: | Nature Communications |
| Online Access: | https://doi.org/10.1038/s41467-024-55581-4 |
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| author | Yarong Wu Youquan Xin Xiaoyan Yang Kai Song Qingwen Zhang Haihong Zhao Cunxiang Li Yong Jin Yan Guo Yafang Tan Yajun Song Huaiyu Tian Zhizhen Qi Ruifu Yang Yujun Cui |
| author_facet | Yarong Wu Youquan Xin Xiaoyan Yang Kai Song Qingwen Zhang Haihong Zhao Cunxiang Li Yong Jin Yan Guo Yafang Tan Yajun Song Huaiyu Tian Zhizhen Qi Ruifu Yang Yujun Cui |
| author_sort | Yarong Wu |
| collection | DOAJ |
| description | Abstract The relative contributions of mutation rate variation, selection, and recombination in shaping genomic variation in bacterial populations remain poorly understood. Here we analyze 3318 Yersinia pestis genomes, spanning nearly a century and including 2336 newly sequenced strains, to shed light on the patterns of genetic diversity and variation distribution at the population level. We identify 45 genomic regions (“hot regions”, HRs) that, although comprising a minor fraction of the genome, are hotbeds of genetic variation. These HRs are distributed non-randomly across Y. pestis phylogenetic lineages and are primarily linked to regulatory genes, underscoring their potential functional significance. We explore various factors contributing to the shaping and maintenance of HRs, including genomic context, homologous recombination, mutation rate variation and natural selection. Our findings suggest that positive selection is likely the primary driver behind the emergence of HRs, but not the sole force, as evidenced by the pronounced trend of variation purging within these regions. |
| format | Article |
| id | doaj-art-24f8ea4d6dd844adbd77f5a02a5c58aa |
| institution | Kabale University |
| issn | 2041-1723 |
| language | English |
| publishDate | 2025-01-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Nature Communications |
| spelling | doaj-art-24f8ea4d6dd844adbd77f5a02a5c58aa2025-01-05T12:41:05ZengNature PortfolioNature Communications2041-17232025-01-0116111310.1038/s41467-024-55581-4Hotspots of genetic change in Yersinia pestisYarong Wu0Youquan Xin1Xiaoyan Yang2Kai Song3Qingwen Zhang4Haihong Zhao5Cunxiang Li6Yong Jin7Yan Guo8Yafang Tan9Yajun Song10Huaiyu Tian11Zhizhen Qi12Ruifu Yang13Yujun Cui14State Key Laboratory of Pathogen and Biosecurity, Academy of Military Medical SciencesKey Laboratory of National Health Commission on Plague Control and Prevention, Key Laboratory for Plague Prevention and Control of Qinghai Province, Qinghai Institute for Endemic Disease Prevention and ControlKey Laboratory of National Health Commission on Plague Control and Prevention, Key Laboratory for Plague Prevention and Control of Qinghai Province, Qinghai Institute for Endemic Disease Prevention and ControlState Key Laboratory of Pathogen and Biosecurity, Academy of Military Medical SciencesKey Laboratory of National Health Commission on Plague Control and Prevention, Key Laboratory for Plague Prevention and Control of Qinghai Province, Qinghai Institute for Endemic Disease Prevention and ControlKey Laboratory of National Health Commission on Plague Control and Prevention, Key Laboratory for Plague Prevention and Control of Qinghai Province, Qinghai Institute for Endemic Disease Prevention and ControlKey Laboratory of National Health Commission on Plague Control and Prevention, Key Laboratory for Plague Prevention and Control of Qinghai Province, Qinghai Institute for Endemic Disease Prevention and ControlKey Laboratory of National Health Commission on Plague Control and Prevention, Key Laboratory for Plague Prevention and Control of Qinghai Province, Qinghai Institute for Endemic Disease Prevention and ControlState Key Laboratory of Pathogen and Biosecurity, Academy of Military Medical SciencesState Key Laboratory of Pathogen and Biosecurity, Academy of Military Medical SciencesState Key Laboratory of Pathogen and Biosecurity, Academy of Military Medical SciencesState Key Laboratory of Remote Sensing Science, Center for Global Change and Public Health, Beijing Normal UniversityKey Laboratory of National Health Commission on Plague Control and Prevention, Key Laboratory for Plague Prevention and Control of Qinghai Province, Qinghai Institute for Endemic Disease Prevention and ControlState Key Laboratory of Pathogen and Biosecurity, Academy of Military Medical SciencesState Key Laboratory of Pathogen and Biosecurity, Academy of Military Medical SciencesAbstract The relative contributions of mutation rate variation, selection, and recombination in shaping genomic variation in bacterial populations remain poorly understood. Here we analyze 3318 Yersinia pestis genomes, spanning nearly a century and including 2336 newly sequenced strains, to shed light on the patterns of genetic diversity and variation distribution at the population level. We identify 45 genomic regions (“hot regions”, HRs) that, although comprising a minor fraction of the genome, are hotbeds of genetic variation. These HRs are distributed non-randomly across Y. pestis phylogenetic lineages and are primarily linked to regulatory genes, underscoring their potential functional significance. We explore various factors contributing to the shaping and maintenance of HRs, including genomic context, homologous recombination, mutation rate variation and natural selection. Our findings suggest that positive selection is likely the primary driver behind the emergence of HRs, but not the sole force, as evidenced by the pronounced trend of variation purging within these regions.https://doi.org/10.1038/s41467-024-55581-4 |
| spellingShingle | Yarong Wu Youquan Xin Xiaoyan Yang Kai Song Qingwen Zhang Haihong Zhao Cunxiang Li Yong Jin Yan Guo Yafang Tan Yajun Song Huaiyu Tian Zhizhen Qi Ruifu Yang Yujun Cui Hotspots of genetic change in Yersinia pestis Nature Communications |
| title | Hotspots of genetic change in Yersinia pestis |
| title_full | Hotspots of genetic change in Yersinia pestis |
| title_fullStr | Hotspots of genetic change in Yersinia pestis |
| title_full_unstemmed | Hotspots of genetic change in Yersinia pestis |
| title_short | Hotspots of genetic change in Yersinia pestis |
| title_sort | hotspots of genetic change in yersinia pestis |
| url | https://doi.org/10.1038/s41467-024-55581-4 |
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