Global diversity and distribution of prophages are lineage-specific within the Ralstonia solanacearum plant pathogenic bacterium species complex
Global diversity and distribution of prophages are lineage-specific within the Ralstonia solanacearum plant pathogenic bacterium species complex
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DOI：
10.1101/2021.10.20.465097
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发表时间：
2021-10
期刊：
影响因子：
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通讯作者：
Samuel T. E. Greenrod;Martina Stoycheva;J. Elphinstone;Ville‐Petri Friman
中科院分区：
文献类型：
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作者：
Samuel T. E. Greenrod;Martina Stoycheva;J. Elphinstone;Ville‐Petri Friman
青枯菌是一种破坏性的植物病原菌，是青枯病的病原菌，侵染全世界200多种植物。除染色体基因外，其毒力还由可移动的遗传元件介导，包括整合的噬菌体DNA，即前驱噬菌体，它可能携带适合性相关的辅助基因或调节宿主基因的表达。虽然实验研究已经确定了几个形成青枯病菌毒力的前驱噬菌体的特征，但青枯菌前驱体的全球多样性、分布和更广泛的功能基因含量尚不清楚。在这项研究中，从来自六大洲的192个青枯病菌基因组草稿组合的不同集合中鉴定了前驱体。通过生物信息学鉴定前驱体，并使用遗传距离、基因含量、GC和总长度来研究它们的多样性。利用青枯丝核菌地理起源和谱系分类(系统类型)的元数据来描述原噬菌体的分布，并通过识别可能的原噬菌体编码的辅助基因来评估它们的功能基因含量。总共鉴定了343个完整的先知，形成了10个不同的基因簇。其中包括五个属于Inoviridae、Myoviridae和Siphopviridae噬菌体家族的前噬菌体簇，以及五个可能代表新的、以前未描述的噬菌体的特征簇。先知有广泛的地理分布，存在于多个大陆。然而，它们通常是宿主系统发育谱系特有的，总体上，原噬菌体多样性与其宿主的遗传多样性成正比。这些前驱体包含无数的辅助基因，这些辅助基因与噬菌体和细菌的新陈代谢和毒力有关。我们的结果表明，虽然青枯病菌的前驱噬菌体在全球范围内高度多样化，但它们对青枯菌辅助基因组的贡献具有谱系特异性，这可能是共同进化历史的结果。
Ralstonia solanacearum is a destructive plant pathogenic bacterium and the causative agent of bacterial wilt disease, infecting over 200 plant species worldwide. In addition to chromosomal genes, its virulence is mediated by mobile genetic elements including integrated DNA of bacteriophages, i.e., prophages, which may carry fitness-associated auxiliary genes or modulate host gene expression. Although experimental studies have characterised several prophages that shape R. solanacearum virulence, the global diversity, distribution, and wider functional gene content of R. solanacearum prophages is unknown. In this study, prophages were identified in a diverse collection of 192 R. solanacearum draft genome assemblies originating from six continents. Prophages were identified bioinformatically and their diversity investigated using genetic distance measures, gene content, GC, and total length. Prophage distribution was characterised using metadata on R. solanacearum geographic origin and lineage classification (phylotypes), and their functional gene content was assessed by identifying putative prophage-encoded auxiliary genes. In total, 343 intact prophages were identified, forming ten genetically distinct clusters. These included five prophage clusters belonging to the Inoviridae, Myoviridae, and Siphoviridae phage families, and five uncharacterised clusters, possibly representing novel, previously undescribed phages. The prophages had broad geographical distribution being present across multiple continents. However, they were generally host phylogenetic lineage-specific, and overall, prophage diversity was proportional to the genetic diversity of their hosts. The prophages contained a myriad of auxiliary genes involved in metabolism and virulence of both phage and bacteria. Our results show that while R. solanacearum prophages are highly diverse globally, they make lineage-specific contributions to the R. solanacearum accessory genome, which could have resulted from shared coevolutionary history.