Pangenomic type III effector database of the plant pathogenic Ralstonia spp.
- Published
- Accepted
- Subject Areas
- Agricultural Science, Bioinformatics, Genomics, Microbiology, Plant Science
- Keywords
- bacterial wilt, type III effector, Ralstonia solanacearum species complex
- Copyright
- © 2019 Sabbagh et al.
- Licence
- This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, reproduction and adaptation in any medium and for any purpose provided that it is properly attributed. For attribution, the original author(s), title, publication source (PeerJ Preprints) and either DOI or URL of the article must be cited.
- Cite this article
- 2019. Pangenomic type III effector database of the plant pathogenic Ralstonia spp. PeerJ Preprints 7:e27726v1 https://doi.org/10.7287/peerj.preprints.27726v1
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.
Author Comment
This is a submission to PeerJ for review.
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.
