Phylogeny and population structure of brown rot- and Moko disease-causing strains of Ralstonia solanacearum phylotype II

Abstract

The ancient soilborne plant vascular pathogen Ralstonia solanacearum has evolved and adapted to cause severe damage in an unusually wide range of plants. In order to better describe and understand these adaptations, strains with very similar lifestyles and host specializations are grouped into ecotypes. We used comparative genomic hybridization (CGH) to investigate three particular ecotypes in the American phylotype II group: (i) brown rot strains from phylotypes IIB-1 and IIB-2, historically known as race 3 biovar 2 and clonal; (ii) new pathogenic variants from phylotype IIB-4NPB that lack pathogenicity for banana but can infect many other plant species; and (iii) Moko disease-causing strains from phylotypes IIB-3, IIB-4, and IIA-6, historically known as race 2, that cause wilt on banana, plantain, and Heliconia spp. We compared the genomes of 72 R. solanacearum strains, mainly from the three major ecotypes of phylotype II, using a newly developed pangenomic microarray to decipher their population structure and gain clues about the epidemiology of these ecotypes. Strain phylogeny and population structure were reconstructed. The results revealed a phylogeographic structure within brown rot strains, allowing us to distinguish European outbreak strains of Andean and African origins. The pangenomic CGH data also demonstrated that Moko ecotype IIB-4 is phylogenetically distinct from the emerging IIB-4NPB strains. These findings improved our understanding of the epidemiology of important ecotypes in phylotype II and will be useful for evolutionary analyses and the development of new DNA-based diagnostic tools.

Fig 1

Depletion curves of the core probe set. The depletion of the core probe set was analyzed for phylotype IIB strains (n = 59) (blue whisker plots) and for the four Ralstonia solanacearum phylotypes (n = 85) (black whisker plots). Each whisker plot represents the distribution of the number of positive probes for a strain of the tested group (size given on the horizontal axis) after 100 resamplings.

Fig 2

(A) Phylogenetic tree of 72 Ralstonia solanacearum strains, computed by MrBayes, version 3.2. Blue numbers and black circles represent statistical support levels below 0.99; red stars indicate the main node for every phylotype. For each strain, the phylotype and sequevar (in parentheses) are given, along with the country and host of isolation. Moko disease strains are shown in boldface. Brown rot strains belong to phylotypes IIB-1 and IIB-2. Squares indicate repetitions of genomic DNA hybridization. (B) Population structure analysis. Each box represents an independent analysis of all R. solanacearum strains (box outlined in red), brown rot strains from phylotypes IIB-1 and IIB-2 (boxes outlined in light or dark blue), or Moko disease-causing strains from phylotypes IIA-6, IIB-3, and IIB-4 (boxes outlined in light or dark green). Within an analysis, each solid bar represents the proportions of ancestral nucleotides inherited from each of the inferred ancestral populations.