Small Insertions and Deletions Drive Genomic Plasticity during Adaptive Evolution of Yersinia pestis

作者：Yarong Wu, Tongyu Hao, Xiuwei Qian, Xianglilan Zhang, Yajun Song, Ruifu Yang, Yujun Cui · 发表于：Microbiology Spectrum · 年份：2022 · DOI：10.1128/spectrum.02242-21 · 被引用次数：11 · 研究领域：Yersinia bacterium, plague, ectoparasites research、Bacillus and Francisella bacterial research、Evolution and Genetic Dynamics

Yersinia pestis, the causative agent of plague, is a highly pathogenic clone of Yersinia pseudotuberculosis. Previous genome-wide SNP analysis provided few adaptive signatures during its evolution. Here by investigating 365 public genomes of Y. pestis, we give a comprehensive overview of general features of genome-wide indels on the core genome and their roles in Y. pestis evolution. Detection of "indel pockets," with average complexity scores declining around indel positions, in both Mycobacterium tuberculosis and Y. pestis, gives us a clue that this phenomenon might appear in other bacterial genomes. Importantly, the identification of four different forms of selection signals in indels would improve our understanding on adaptive evolution of Y. pestis, and provide targets for further physiological mechanism researches of this pathogen. As evolutionary research based on genome-wide indels is still rare in bacteria, our study would be a helpful reference in deciphering the role of indels in other species.