Geng Ruimei, Cheng Lirui, Cao Changdai, Liu Zhengwen, Liu Dan, Xiao Zhiliang, Wu Xiuming, Huang Zhenrui, Feng Quanfu, Luo Chenggang, Chen Zhiqiang, Zhang Zhenchen, Jiang Caihong, Ren Min, Yang Aiguo
Key Laboratory for Tobacco Gene Resources, Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, China.
Shandong Rizhao Tobacco Company Ltd., Rizhao, China.
Front Microbiol. 2022 May 6;13:854792. doi: 10.3389/fmicb.2022.854792. eCollection 2022.
species complex (RSSC) is a diverse group of plant pathogens that attack a wide range of hosts and cause devastating losses worldwide. In this study, we conducted a comprehensive analysis of 131 RSSC strains to detect their genetic diversity, pathogenicity, and evolution dynamics. Average nucleotide identity analysis was performed to explore the genomic relatedness among these strains, and finally obtained an open pangenome with 32,961 gene families. To better understand the diverse evolution and pathogenicity, we also conducted a series of analyses of virulence factors (VFs) and horizontal gene transfer (HGT) in the pangenome and at the single genome level. The distribution of VFs and mobile genetic elements (MGEs) showed significant differences among different groups and strains, which were consistent with the new nomenclatures of the RSSC with three distinct species. Further functional analysis showed that most HGT events conferred from and played a great role in shaping the genomic plasticity and genetic diversity of RSSC genomes. Our work provides insights into the genetic polymorphism, evolution dynamics, and pathogenetic variety of RSSC and provides strong supports for the new taxonomic classification, as well as abundant resources for studying host specificity and pathogen emergence.
锈腐病菌复合种（RSSC）是一类多样的植物病原体，可侵染多种寄主并在全球范围内造成毁灭性损失。在本研究中，我们对131个RSSC菌株进行了全面分析，以检测它们的遗传多样性、致病性和进化动态。进行了平均核苷酸同一性分析以探索这些菌株之间的基因组相关性，最终获得了一个包含32,961个基因家族的开放泛基因组。为了更好地理解其多样的进化和致病性，我们还在泛基因组和单基因组水平上对毒力因子（VFs）和水平基因转移（HGT）进行了一系列分析。毒力因子和移动遗传元件（MGEs）的分布在不同组和菌株之间显示出显著差异，这与具有三个不同物种的RSSC的新命名法一致。进一步的功能分析表明，大多数HGT事件源自并在塑造RSSC基因组的基因组可塑性和遗传多样性方面发挥了重要作用。我们的工作为RSSC的遗传多态性、进化动态和致病多样性提供了见解，并为新的分类学分类提供了有力支持，以及为研究寄主特异性和病原体出现提供了丰富资源。
