Pangenomic type III effector database of the plant pathogenic Ralstonia spp.
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Abstract
Background. The bacterial plant pathogenic Ralstonia species belong to the beta-proteobacteria order and are soil-borne pathogens causing the vascular bacterial wilt disease, affecting a wide range of plant hosts. These bacteria form a heterogeneous group considered as a “species complex”,” gathering three newly defined species. Like many other Gram negative plant pathogens, Ralstonia pathogenicity relies on a type III secretion system, enabling bacteria to secrete/inject a large repertoire of type III effectors into their plant host cells. T3Es are thought to participate in generating a favorable environment for the pathogen (countering plant immunity and modifying the host metabolism and physiology). Methods. Expert genome annotation, followed by specific type III-dependent secretion, allowed us to improve our Hidden-Markov-Model and Blast profiles for the prediction of type III effectors. Results. We curated the T3E repertoires of 12 plant pathogenic Ralstoniastrains, representing a total of 12 strains spread over the different groups of the species complex. This generated a pangenome repertoire of 102 T3E genes and 16 hypothetical T3E genes. Using this database, we scanned for the presence of T3Es in the 155 available genomes representing 140 distinct plant pathogenic Ralstonia strains isolated from different host plants in different areas of the globe. All this information is presented in a searchable database. A presence/absence analysis, modulated by a strain sequence/gene annotation quality score, enabled us to redefine core and accessory T3E repertoires.
Cite this as
2019. Pangenomic type III effector database of the plant pathogenic Ralstonia spp. PeerJ Preprints 7:e27726v1 https://doi.org/10.7287/peerj.preprints.27726v1note This preprint is not peer-reviewed. You may wish to reference the subsequent peer-reviewed version of this article.
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This is a submission to PeerJ for review.
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Supplemental Information
mutS alignment and phylogenetic tree on the set of 140 different strains
A neighbor-joining tree was build using the mutS from Ralstonia pickettii as an outgroup. Bootstrap were performed on 100 replicates, only support higher than 50% displayed in the consensus tree.
Additional Information
Competing Interests
The authors declare that they have no competing interests.
Author Contributions
Cyrus Raja Rubenstein Sabbagh conceived and designed the experiments, performed the experiments, analyzed the data, prepared figures and/or tables, authored or reviewed drafts of the paper, approved the final draft.
Sébastien Carrère conceived and designed the experiments, performed the experiments, analyzed the data, prepared figures and/or tables, authored or reviewed drafts of the paper, approved the final draft.
Fabien Lonjon conceived and designed the experiments, performed the experiments, analyzed the data, prepared figures and/or tables, authored or reviewed drafts of the paper, approved the final draft.
Fabienne Vailleau conceived and designed the experiments, analyzed the data, authored or reviewed drafts of the paper, approved the final draft.
Alberto P Macho conceived and designed the experiments, analyzed the data, contributed reagents/materials/analysis tools, authored or reviewed drafts of the paper, approved the final draft.
Stephane Genin conceived and designed the experiments, performed the experiments, analyzed the data, prepared figures and/or tables, authored or reviewed drafts of the paper, approved the final draft.
Nemo Peeters conceived and designed the experiments, performed the experiments, analyzed the data, prepared figures and/or tables, authored or reviewed drafts of the paper, approved the final draft.
Data Deposition
The following information was supplied regarding data availability:
The raw data, i.e. the genomes of the 155 strains are publicly available in GenBank and references thereof have been entered in our Table S1, which also contains all the metadata necessary for redoing the analysis. On our https://iant.toulouse.inra.fr/T3E (maintained now since 2013, and will continue to be), one can download all the data using specific queries. Raw data files are also available (whole genome prediction files).
Funding
CRRS was funded by grants from Lebanon (the municipality of Nabatieh and the association for scientific orientation and specialization). APM is supported by the Shanghai Center for Plant Stress Biology (Chinese Academy of Sciences) and the Chinese 1000 Talents Program. We also received funding from the Laboratoire d’Excellence (LABEX) TULIP (ANR-10-LABX-41). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
