ArticleNature communications2025
Hotspots of genetic change in Yersinia pestis.
Article in Nature communications, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
What it found
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
12 citing papers in PubMed.
- A field-deployable high-resolution SNP genotyping platform for rapid surveillance ofVirulence · 2026Article
- A prehistoric East-Asian Yersinia pestis genome and a ~5.3 ka trans-Eurasian expansion of plague.Nature communications · 2026Article
- Temperature-dependent dynamics of DNA methylation and plasmid copy number in Yersinia pestis.BMC genomics · 2026Article
- Molecular diversity and phylogenetic characterization of theVeterinary world · 2026Article
- Genomic diversification and tailocin-mediated competition in animal-associatedISME communications · 2026Article
- Characterization of YhcN in stress adaptation and its complex transcriptional regulation by SlyA inFrontiers in cellular and infection microbiology · 2026Article
- Retracing the path of evolution: polymorphisms ofEmerging microbes & infections · 2025Article
- Evaluating the early diversification of Yersinia pestis and its phylogeographic expansion over 96 years of evolution in Madagascar.Communications biology · 2025Article
- Evolutionary hotspots in bacterial genomes.Nature reviews. Microbiology · 2025Article
- Insights into Yersinia pestis evolution through rearrangement analysis of 242 complete genomes.Nature genetics · 2025Article
- Outer membrane vesicles in gram-negative bacteria and its correlation with pathogenesis.Frontiers in immunology · 2025Review
- Systematic analysis of spontaneous tandem genome amplification events in Yersinia pestis.PloS one · 2025Article
Corrections and comments
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Authors and funding
15 authors.
Funding
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.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the Socratic graph.