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The original resource can be found HERE .

EuroXanth DokuWiki on diagnostic tools, virulence factors and resistance genes

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

Bacterial virulence factors

Plant resistance genes

Please also note the following publication related to this EuroXanth DokuWiki and do not hesitate to cite it if you find it useful in your work:

Costa J, Pothier JF, Bosis E, Boch J, Kölliker R, Koebnik R (2024). A community-curated DokuWiki resource on diagnostics, diversity, pathogenicity, and genetic control of xanthomonads. Mol. Plant Microbe Interact. 37: 347-353. DOI: 10.1094/MPMI-11-23-0184-FI

Other resources:

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)

NCBI Batch Entrez tutorial

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 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

start.txt · Last modified: 2024/06/10 13:53 by rkoebnik