Jiang Wanyue, Pan Jiao, Lin Tongtong, Wang Yaohai, Wang Yanze, Zhang Rongxiao, Zhou Xiaoming, Zhang Yu
Key Laboratory of Evolution and Marine Biodiversity (Ministry of Education), Institute of Evolution and Marine Biodiversity, KLMME, Ocean University of China, Qingdao, Shandong, China.
Laboratory for Marine Biology and Biotechnology, Qingdao Marine Science and Technology Center, Qingdao, Shandong, China.
Microbiol Spectr. 2025 May 6;13(5):e0212724. doi: 10.1128/spectrum.02127-24. Epub 2025 Mar 25.
The genomes of multi-replicon bacteria are composed of a primary replicon (the chromosome) and secondary replicons (chromids). Currently, there is a lack of understanding of the mutation features and evolutionary patterns of these different replicons. Specifically, in the genus , the chromids of multi-replicon species exhibit both unidirectional and bidirectional replication. Here, we investigated the similarities and differences between chromosomes and chromids in sequence composition and gene synteny of species by comparative genomic analysis, as well as the spontaneous mutation features of different replicons by mutation accumulation (MA) experiments combined with whole-genome sequencing strategy (MA-WGS). MA-WGS analysis revealed that there was no significant difference between chromids and chromosomes in the mutation rate or mutation spectrum of . sp. LC0214 (where the chromid is unidirectional in replication) and . sp. JCM12884 (where the chromid is bidirectional in replication). In addition, the context-dependence and variation pattern of the base-pair substitutions (BPSs) rates of the entire replicons exhibited differences that may be caused by the different replication directions of the chromids. The results of this study provide a new theoretical foundation for an in-depth understanding of the origin and evolution of chromids in multi-replicon bacterial species and facilitate further exploration of the complex mechanisms of bacterial diversity.IMPORTANCE mutations are a critical driving force in species evolution. Currently, there is a lack of sufficient research on the influence of replicon types on the occurrence of genomic mutations in bacteria. Moreover, the scarcity in systematic analysis and comparison of spontaneous mutation features between different replicons results in the limited information on the evolutionary dynamics of multi-replicon species. The diversity of replication direction in the multi-replicon species of the genus provides a unique opportunity for studying the impact of replication direction on the patterns of mutation. In addition to the composition characteristics between chromosomes and chromids, the spontaneous mutation rates in the context-dependence and variation pattern of the base-pair substitutions (BPSs) across different replicons within species revealed in this study provide valuable insights into the evolutionary dynamics of bacterial secondary replicons.
多复制子细菌的基因组由一个主要复制子（染色体）和多个次要复制子（染色体外遗传因子）组成。目前，人们对这些不同复制子的突变特征和进化模式缺乏了解。具体而言，在某一属中，多复制子物种的染色体外遗传因子呈现单向和双向复制。在此，我们通过比较基因组分析研究了某物种染色体和染色体外遗传因子在序列组成和基因同线性方面的异同，并通过突变积累（MA）实验结合全基因组测序策略（MA-WGS）研究了不同复制子的自发突变特征。MA-WGS分析显示，在某菌属的LC0214菌株（其染色体外遗传因子为单向复制）和JCM12884菌株（其染色体外遗传因子为双向复制）中，染色体外遗传因子和染色体在突变率或突变谱上没有显著差异。此外，整个复制子的碱基对替换（BPS）率的上下文依赖性和变化模式表现出差异，这可能是由染色体外遗传因子不同的复制方向导致的。本研究结果为深入了解多复制子细菌物种中染色体外遗传因子的起源和进化提供了新的理论基础，并有助于进一步探索细菌多样性的复杂机制。重要性 突变是物种进化的关键驱动力。目前，关于复制子类型对细菌基因组突变发生的影响缺乏足够的研究。此外，对不同复制子之间自发突变特征的系统分析和比较较少，导致关于多复制子物种进化动态的信息有限。某属多复制子物种中复制方向的多样性为研究复制方向对突变模式的影响提供了独特的机会。除了染色体和染色体外遗传因子之间的组成特征外，本研究揭示的某物种不同复制子中碱基对替换（BPS）的上下文依赖性和变化模式中的自发突变率，为细菌次要复制子的进化动态提供了有价值的见解。
