Elphinstone, J. | bioRxiv Science

bioRxiv2022

Influence of insertion sequences on population structure of phytopathogenic bacteria in the Ralstonia solanacearum species complex

Ralstonia solanacearum species complex (RSSC) is a destructive group of plant pathogenic bacteria and the causative agent of bacterial wilt disease. Experimental studies have attributed RSSC virulence to insertion sequences (IS), transposable genetic elements which can both disrupt and activate host genes. Yet, the global diversity and distribution of RSSC IS are unknown. In this study, IS were bioinformatically identified in a diverse collection of 356 RSSC strains representing four phylogenetic lineages, and their diversity investigated based on genetic distance measures and comparisons with the ISFinder database. IS distributions were characterised using metadata on RSSC lineage classification and potential gene disruptions by IS were determined based on their proximity to coding sequences. In total, we found 24,732 IS belonging to eleven IS families and 26 IS subgroups, with over half of the IS found in the megaplasmid. While IS families were generally widespread across the RSSC phylogeny, IS subgroups showed strong lineage-specific distributions and genetically similar bacterial strains had similar IS contents. Further, IS present in multiple lineages were generally found in different genomic regions suggesting potential recent horizontal transfer. Finally, IS were found to disrupt many genes with predicted functions in virulence, stress tolerance, and metabolism, suggesting that they might be adaptive. This study highlights that RSSC insertion sequences track the evolution of their bacterial hosts, potentially contributing to both intra- and inter-lineage genetic diversity.

genomics↗

bioRxiv2021

Global diversity and distribution of prophages is lineage-specific within the Ralstonia solanacearum plant pathogenic bacterium species complex

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.

microbiology↗