Comparative genomic analysis of Ralstonia solanacearum reveals candidate genes for host specificity

Abstract

BackgroundRalstonia solanacearum is a vascular soil-borne plant pathogen with an unusually broad host range. This economically destructive and globally distributed bacterium has thousands of distinct lineages within a heterogeneous and taxonomically disputed species complex. Some lineages include highly host-adapted strains (ecotypes), such as the banana Moko disease-causing strains, the cold-tolerant potato brown rot strains (also known as R3bv2) and the recently emerged Not Pathogenic to Banana (NPB) strains.ResultsThese distinct ecotypes offer a robust model to study host adaptation and the emergence of ecotypes because the polyphyletic Moko strains include lineages that are phylogenetically close to the monophyletic brown rot and NPB strains. Draft genomes of eight new strains belonging to these three model ecotypes were produced to complement the eleven publicly available R. solanacearum genomes. Using a suite of bioinformatics methods, we searched for genetic and evolutionary features that distinguish ecotypes and propose specific hypotheses concerning mechanisms of host adaptation in the R. solanacearum species complex. Genome-wide, few differences were identified, but gene loss events, non-synonymous polymorphisms, and horizontal gene transfer were identified among type III effectors and were associated with host range differences.ConclusionsThis extensive comparative genomics analysis uncovered relatively few divergent features among closely related strains with contrasting biological characteristics; however, several virulence factors were associated with the emergence of Moko, NPB and brown rot and could explain host adaptation.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-1474-8) contains supplementary material, which is available to authorized users.

Characterization of CRISPR‐Cas systems in the Ralstonia solanacearum species complex

“…Therefore, the expression profile of the cas genes from RSSC strains may be different in the natural environment. Previous transcriptomic studies have shown that gene expression profiles of RSSC strains drastically change in plants when compared with growth in a synthetic rich medium (Ailloud et al , ; Jacobs et al , ; Puigvert et al , ).…”

Plant–phytopathogen interactions: bacterial responses to environmental and plant stimuli

“…This large host range, and broad geographic distribution, explains the severe worldwide crop losses caused by this pathogen. Genomic analysis of the more than 40 sequenced R. solanacearum strains reveals that it forms a species complex containing four phylotypes, correlated with strain geographic origin, and this may partially account for the group's broad host range (Genin and Denny, ; Remenant et al ., ; Ailloud et al ., ; Prior et al ., ).…”

“…In banana plants, the Moko strain differentially up‐regulated siderophore biosynthesis and nitrate assimilation genes, whereas in melon plants the NPB strain differentially up‐regulated expression of type III effectors and denitrification genes. Despite a high conservation of genomic content between these two strains (90% of genes in common; (Ailloud et al ., ), the differential gene expression associated with host variation suggests that each pathotype is sensitive, to varying degrees, to stimuli dependent on the infected host.…”

Genomic Analysis of Phylotype I Strain EP1 Reveals Substantial Divergence from Other Strains in the Ralstonia solanacearum Species Complex

“…For example, recent genomic and proteomic comparisons suggested the separation of the R. solanacearum species complex into three species, namely the original phylotype II, phylotype IV, and the union of phylotype I and III (Prior et al, 2016). Furthermore, comparative genomic analysis have also uncovered some divergent features among closely related strains, including putative virulence effectors associated with host adaptation(Ailloud et al, 2015), and presented evidences on the horizontal gene transfer between R. solanacearum strains (Guidot et al, 2009). …”