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--- diagnostics [2022/10/06 21:32] – jfpothier
+++ diagnostics [2023/10/01 17:17] (current) – [Other resources:] rkoebnik
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-  * [[diagnostics:disease_regulation_management|Diseases, regulation and recommendations for management of phytosanitary-regulated //Xanthomonas// in the European Union]]
+====== Molecular Diagnosis and Diversity for Regulated Xanthomonas ======
-  * [[diagnostics:dna_protocols|Diagnostics: main protocols based on amplification of specific target DNAs]]
-  * [[typing:molecular_typing|Diversity: tools for molecular typing]]
+This data is based on the review by [[https://doi.org/10.3390/microorganisms9040862|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 [[https://euroxanth.eu/management/wg1|Working Group 1]] 'Diagnostics & Diversity–Population Structure' from the [[https://euroxanth.eu|EuroXanth]] COST Action CA16107.
+Specifically, we provide information on:
+  * [[:diagnostics:disease_regulation_management|Diseases, regulation and recommendations for management of phytosanitary-regulated //Xanthomonas// in the European Union]]
+  * [[:diagnostics:dna_protocols|Diagnostics: main protocols based on amplification of specific target DNAs]]
+  * [[:typing:molecular_typing|Diversity: tools for molecular typing]]
+===== Other resources: =====
+[[https://linbase.org/LINbase/|LINbase]] - The Life Identification Number<sup>®</sup>  (LIN<sup>®</sup>  ) Platform (Tian //et al.//, 2020)
+[[https://microbesgenotyping.i2bc.paris-saclay.fr/|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)
+[[http://genome.ppws.vt.edu/cgi-bin/MLST/home.pl|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)
+[[https://phytobacexplorer.warwick.ac.uk|PhytoBacExplorer]] - Online resource for analysing and visualising genomic variation within plant-pathogenic bacteria
+[[https://pubmlst.org/|PubMLST]] - A collection of open-access, curated databases that integrate population sequence data (e.g., //Xanthomonas citri//, //Xylella fastidiosa//) (Jolley //et al.//, 2018)
+===== References =====
+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: [[https://doi.org/10.1094/PHYTO-100-3-0208|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: [[https://doi.org/10.3390/microorganisms9040862|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: [[https://doi.org/10.1016/j.biochi.2007.07.014|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: [[https://doi.org/10.12688/wellcomeopenres.14826.1|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: [[https://doi.org/10.1093/nar/gkaa190|10.1093/nar/gkaa190]]

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