Repertoire, unified nomenclature and evolution of the Type III effector gene set in the Ralstonia solanacearum species complex

Background: Ralstonia solanacearum is a soil-borne
beta-proteobacterium that causes bacterial wilt disease in many
food crops and is a major problem for agriculture in intertropical
regions. R. solanacearum is a heterogeneous species, both
phenotypically and genetically, and is considered as a species
complex. Pathogenicity of R. solanacearum relies on the Type III
secretion system that injects Type III effector (T3E) proteins into
plant cells. T3E collectively perturb host cell processes and
modulate plant immunity to enable bacterial infection. Results: We
provide the catalogue of T3E in the R. solanacearum species
complex, as well as candidates in newly sequenced strains. 94 T3E
orthologous groups were defined on phylogenetic bases and ordered
using a uniform nomenclature. This curated T3E catalog is available
on a public website and a bioinformatic pipeline has been designed
to rapidly predict T3E genes in newly sequenced strains.
Systematical analyses were performed to detect lateral T3E gene
transfer events and identify T3E genes under positive selection.
Our analyses also pinpoint the RipF translocon proteins as major
discriminating determinants among the phylogenetic lineages.
Conclusions: Establishment of T3E repertoires in strains
representatives of the R. solanacearum biodiversity allowed
determining a set of 22 T3E present in all the strains but provided
no clues on host specificity determinants. The definition of a
standardized nomenclature and the optimization of predictive tools
will pave the way to understanding how variation of these
repertoires is correlated to the diversification of this species
complex and how they contribute to the different strain pathotypes.