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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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This data is based on the review by Catara et al. (2021), focused on the molecular methods for diagnosis, detection, and studies on the diversity of plant pathogenic Xanthomonas, concentrating especially on regulated pathogens in the European Union published as a collective effort of the Working Group 1 'Diagnostics & Diversity–Population Structure' from the EuroXanth COST Action CA16107.
Specifically, we provide information on:
LINbase - The Life Identification Number® (LIN® ) Platform (Tian et al., 2020)
MLVAbank - A genotyping resource for tandem repeat typing (MLVA for Multiple Loci VNTR analysis), CRISPR typing (CRISPR for Clustered Regularly Interspaced Short Palindromic Repeats), sequence typing (MLST for Multiple Loci Sequence Typing) and Single Nucleotide Polymorphisms (SNP) (e.g., Xanthomonas fragariae) (Grissa et al., 2008)
PAMDB - A multilocus sequence typing and analysis (MLST/MLSA) website and database specifically designed for identification of plant associated and environmental microbes and for the study of their epidemiology, population genetics, and molecular evolution (Almeida et al., 2010)
PhytoBacExplorer - Online resource for analysing and visualising genomic variation within plant-pathogenic bacteria
PubMLST - A collection of open-access, curated databases that integrate population sequence data (e.g., Xanthomonas citri, Xylella fastidiosa) (Jolley et al., 2018)
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
Catara V, Cubero J, Pothier JF, Bosis E, Bragard C, Đermić E, Holeva MC, Jacques MA, Petter F, Pruvost O, Robène I, Studholme DJ, Tavares F, Vicente JG, Koebnik R, Costa J (2021). Trends in molecular diagnosis and diversity studies for phytosanitary regulated Xanthomonas. Microorganisms 9: 862. DOI: 10.3390/microorganisms9040862
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
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
