Differences

This shows you the differences between two versions of the page.

--- start [2022/10/06 16:45] – old revision restored (2022/10/06 17:42) rkoebnik
+++ start [2024/06/10 13:53] (current) – [EuroXanth DokuWiki on diagnostic tools, virulence factors and resistance genes] rkoebnik
@@ Line 1: / Line 1: @@
-The original Xanthomonas.org resource can be found [[http://www.biopred.net/xanthomonas/|HERE]].
+The original **Xanthomonas.org** resource can be found **[[http://www.biopred.net/xanthomonas/|HERE]]** .
-**EuroXanth DokuWiki on virulence factors and resistance genes**
+====== EuroXanth DokuWiki on diagnostic tools, virulence factors and resistance genes ======
+This online resource, which was developed as a collective effort of the [[https://euroxanth.eu|EuroXanth]] COST Action CA16107 (Costa //et al.//, 2021, 2022), provides information on:
+[[:diagnostics|Diagnostic and diversity tools]]
 [[:bacteria:bacterial_virulence_factors|Bacterial virulence factors]]
@@ Line 7: / Line 11: @@
 [[:plant:plant_resistance_genes|Plant resistance genes]]
-**Resources:**
+► **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:**
-[[https://euroxanth.eu/|EuroXanth COST Action CA16107]]
+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: [[https://doi.org/10.1094/MPMI-11-23-0184-FI|10.1094/MPMI-11-23-0184-FI]]
-Type III Effectors @ [[http://www.biopred.net/xanthomonas/t3e.html|Xanthomonas.org]]
+----
-[[https://iant.toulouse.inra.fr/T3E|Ralstonia T3E (Toulouse)]]
+===== Other resources: =====
+[[https://phytobacexplorer.warwick.ac.uk|PhytoBacExplorer]] - Online resource for analysing and visualising genomic variation within plant-pathogenic bacteria
+[[:diagnostics|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)
+[[:bacteria:t3e:t3e|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)
 [[https://www.ncbi.nlm.nih.gov/sites/batchentrez|NCBI Batch Entrez tutorial]]
-[[http://papers.genomics.lbl.gov/|PaperBlast]] - Find papers about a protein or its homologs
+[[http://papers.genomics.lbl.gov/|PaperBlast]] (Price & Arkin, 2017) - Find papers about a protein or its homologs
+===== 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]]
+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: [[https://doi.org/10.1111/mpp.13150|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: [[https://doi.org/10.3390/microorganisms11010006|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: [[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]]
+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: [[https://doi.org/10.1094/MPMI-18-0275|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: [[https://doi.org/10.1186/1471-2164-14-859|10.1186/1471-2164-14-859]]
+Price MN, Arkin AP (2017). PaperBLAST: text mining papers for information about homologs. mSystems 2: e00039-17. DOI: [[https://doi.org/10.1128/mSystems.00039-17|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: [[https://doi.org/10.7717/peerj.7346|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: [[https://doi.org/10.1093/nar/gkaa190|10.1093/nar/gkaa190]]

EuroXanth DokuWiki

User Tools

Site Tools

Differences

Page Tools