Homologous recombination is a major force mechanism driving bacterial evolution, host adaptability and acquisition of novel virulence traits. Pectobacterium parmentieri is a plant bacterial pathogen distributed worldwide, primarily affecting potatoes, by causing soft rot and blackleg diseases. The goal of this investigation was to understand the impact of homologous recombination on the genomic evolution of P. parmentieri. Analysis of P. parmentieri genomes using Roary revealed a dynamic pan-genome with 3,742 core genes and over 55% accessory genome variability. Bayesian population structure analysis identified seven lineages, indicating species heterogeneity. ClonalFrameML analysis displayed 5,125 recombination events, with the lineage 4 exhibiting the highest events. fastGEAR analysis identified 486 ancestral and 941 recent recombination events ranging 43 bp - 119 kb and 36 bp - 13.96 kb, respectively, suggesting ongoing adaptation. Notably, 11% (412 genes) of the core genome underwent recent recombination, with lineage 1 as the main donor. The prevalence of recent recombination (double compared to ancient) events implies continuous adaptation, possibly driven by global potato trade. Recombination events were found in genes involved in vital cellular processes (DNA replication, DNA repair, RNA processing, homeostasis, and metabolism), pathogenicity determinants (type secretion systems, cell-wall degrading enzymes, iron scavengers, lipopolysaccharides, flagellum, etc.), antimicrobial compounds (phenazine and colicin) and even CRISPR-Cas genes. Overall, these results emphasize the potential role of homologous recombination in P. parmentieri’s evolutionary dynamics, influencing host colonization, pathogenicity, adaptive immunity, and ecological fitness.

中文翻译：

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同源重组对帕门氏果杆菌核心基因组进化和宿主适应的影响

同源重组是驱动细菌进化、宿主适应性和获得新毒力性状的主要机制。帕门氏杆菌是一种分布于世界各地的植物细菌病原体，主要影响马铃薯，引起软腐病和黑胫病。本研究的目的是了解同源重组对 P. parmentieri 基因组进化的影响。使用 Roary 对 P. parmentieri 基因组进行分析，揭示了一个动态泛基因组，包含 3,742 个核心基因和超过 55% 的辅助基因组变异性。贝叶斯种群结构分析确定了七个谱系，表明物种异质性。ClonalFrameML 分析显示了 5,125 个重组事件，其中谱系 4 的重组事件最多。fastGEAR 分析确定了 486 个祖先重组事件和 941 个近期重组事件，范围分别为 43 bp - 119 kb 和 36 bp - 13.96 kb，表明正在进行的适应。值得注意的是，11%（412 个基因）的核心基因组最近经历了重组，其中谱系 1 是主要供体。最近重组事件的盛行（与古代相比是两倍）意味着持续的适应，可能是由全球马铃薯贸易驱动的。在参与重要细胞过程（DNA复制、DNA修复、RNA加工、稳态和代谢）、致病性决定因素（类型分泌系统、细胞壁降解酶、铁清除剂、脂多糖、鞭毛等）和致病性决定因素（类型分泌系统、细胞壁降解酶、铁清除剂、脂多糖、鞭毛等）的基因中发现了重组事件。 、抗菌化合物（吩嗪和大肠菌素）甚至 CRISPR-Cas 基因。总体而言，这些结果强调了同源重组在 P. parmentieri 进化动力学中的潜在作用，影响宿主定植、致病性、适应性免疫和生态适应性。