Learn about COST & EuroXanth
Molecular Diagnosis and Diversity for Regulated Xanthomonas
Bacterial virulence factors
This DokuWiki is based upon work from COST Action CA16107 EuroXanth, supported by COST (European Cooperation in Science and Technology)
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The original Xanthomonas.org resource can be found HERE .
This online resource, which was developed as a collective effort of the EuroXanth COST Action CA16107 (Costa et al., 2021, 2022), provides information on:
Diagnostic and diversity tools
PhytoBacExplorer - Online resource for analysing and visualising genomic variation within plant-pathogenic bacteria
Databases for molecular genotyping, e.g. LINbase, MLVAbank, PAMDB, PubMLST (Almeida et al., 2010; Grissa et al., 2008; Jolley et al., 2018; Tian et al., 2020)
Databases for type III effectors, incl. the Pseudomonas syringae and Ralstonia solanacearum species complex (Lindeberg et al., 2005; Peeters et al., 2013; Sabbagh et al., 2019)
PaperBlast (Price & Arkin, 2017) - Find papers about a protein or its homologs
Almeida NF, Yan S, Cai R, Clarke CR, Morris CE, Schaad NW, Schuenzel EL, Lacy GH, Sun X, Jones JB, Castillo JA, Bull CT, Leman S, Guttman DS, Setubal JC, Vinatzer BA (2010). PAMDB, a multilocus sequence typing and analysis database and website for plant-associated microbes. Phytopathology 100: 208-215. DOI: 10.1094/PHYTO-100-3-0208
Costa J, Pothier JF, Boch J, Stefani E, Jacques MA, Catara V, Koebnik R (2021). Integrating science on Xanthomonadaceae for sustainable plant disease management in Europe. Mol. Plant Pathol. 22: 1461-1463. DOI: 10.1111/mpp.13150
Costa J, Pothier JF, Boch J, Stefani E, Koebnik R (2022). Integrating science on Xanthomonas and Xylella for integrated plant disease management. Microorganisms 11: 6. DOI: 10.3390/microorganisms11010006
Grissa I, Bouchon P, Pourcel C, Vergnaud G (2008). On-line resources for bacterial micro-evolution studies using MLVA or CRISPR typing. Biochimie 90: 660-668. DOI: 10.1016/j.biochi.2007.07.014
Jolley KA, Bray JE, Maiden MCJ (2018). Open-access bacterial population genomics: BIGSdb software, the PubMLST.org website and their applications. Wellcome Open Res. 3: 124. DOI: 10.12688/wellcomeopenres.14826.1
Lindeberg M, Stavrinides J, Chang JH, Alfano JR, Collmer A, Dangl JL, Greenberg JT, Mansfield JW, Guttman DS (2005). Proposed guidelines for a unified nomenclature and phylogenetic analysis of type III Hop effector proteins in the plant pathogen Pseudomonas syringae. Mol. Plant Microbe Interact. 18: 275-282. DOI: 10.1094/MPMI-18-0275
Peeters N, Carrère S, Anisimova M, Plener L, Cazalé AC, Genin S (2013). Repertoire, unified nomenclature and evolution of the Type III effector gene set in the Ralstonia solanacearum species complex. BMC Genomics 14: 859. DOI: 10.1186/1471-2164-14-859
Price MN, Arkin AP (2017). PaperBLAST: text mining papers for information about homologs. mSystems 2: e00039-17. DOI: 10.1128/mSystems.00039-17
Sabbagh CRR, Carrere S, Lonjon F, Vailleau F, Macho AP, Genin S, Peeters N (2019). Pangenomic type III effector database of the plant pathogenic Ralstonia spp. PeerJ 7: e7346. DOI: 10.7717/peerj.7346
Tian L, Huang C, Mazloom R, Heath LS, Vinatzer BA (2020). LINbase: a web server for genome-based identification of prokaryotes as members of crowdsourced taxa. Nucleic Acids Res. 48: W529-W537. DOI: 10.1093/nar/gkaa190
