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Open Access Highly Accessed Research article

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

Nemo Peeters12*, Sébastien Carrère12, Maria Anisimova34, Laure Plener125, Anne-Claire Cazalé12 and Stephane Genin12*

Author Affiliations

1 INRA, Laboratoire des Interactions Plantes-Microorganismes (LIPM), UMR441, F-31326 Castanet-Tolosan, France

2 CNRS, Laboratoire des Interactions Plantes-Microorganismes (LIPM), UMR2594, F-31326 Castanet-Tolosan, France

3 Department of Computer Science, ETH Zurich, Zurich, Switzerland

4 Swiss Institute of Bioinformatics, Lausanne, Switzerland

5 Biozentrum, Department Biologie I, Ber. Mikrobiologie, Ludwig-Maximilians Universität Muenchen, Grosshaderner Str. 2-4, 82152 Martiensried, Germany

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BMC Genomics 2013, 14:859  doi:10.1186/1471-2164-14-859

Published: 6 December 2013

Abstract

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.

Keywords:
Type III effector; Ralstonia solanacearum; Selection; Horizontal gene transfer; Host specificity