typing:molecular_typing
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| typing:molecular_typing [2025/02/13 14:30] – [Table] rkoebnik | typing:molecular_typing [2025/02/14 17:19] (current) – [Table] rkoebnik | ||
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| This data is based on the review by [[https:// | This data is based on the review by [[https:// | ||
| - | **Tools for molecular typing of regulated | + | **Tools for molecular typing of regulated |
| - | ^ Pathogen | + | ^ Pathogen |
| - | | **A1 list** | + | | **A1 list** |
| - | | //X. citri// pv. // | + | | //X. citri// pv. // |
| - | | //X. citri// pv. // | + | | //X. citri// pv. // |
| - | | //X. euvesicatoria// | + | | //X. euvesicatoria// |
| - | | //X. oryzae// pv. // | + | | //X. oryzae// pv. // |
| - | | //X. oryzae// pv. // | + | | //X. oryzae// pv. // |
| - | | **A2 list** | + | | **A2 list** |
| - | | //X. arboricola// | + | | //X. arboricola// |
| - | | //X. arboricola// | + | | //X. arboricola// |
| - | | //X. arboricola// | + | | //X. arboricola// |
| - | | //X. axonopodis// | + | | //X. axonopodis// |
| - | | //X. euvesicatoria// | + | | //X. euvesicatoria// |
| - | | //X. euvesicatoria// | + | | //X. euvesicatoria// |
| - | | //X. fragariae// | + | | //X. fragariae// |
| - | | //X. hortorum// pv. // | + | | //X. hortorum// pv. // |
| - | | //X. phaseoli// pv. // | + | | //X. phaseoli// pv. // |
| - | | //X. phaseoli// pv. // | + | | //X. phaseoli// pv. // |
| - | | //X. translucens// | + | | //X. translucens// |
| - | | //X. vesicatoria// | + | | //X. vesicatoria// |
| - | | //Xylella fastidiosa// | + | | //Xylella fastidiosa// |
| + | | **Other** | ||
| + | | //X. phaseoli// pv. // | ||
| < | < | ||
| ===== References ===== | ===== References ===== | ||
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| + | Aguilar-Granados A, Hernández-Macías B, Santiago-Martínez G, Ruiz-Medrano R, Kameyama-Kawabe L, Hinojosa-Moya J, Del Carmen Montes-Horcasitas M, Xoconostle-Cázares B (2021). Genetic diversity of //Xylella fastidiosa// | ||
| + | |||
| + | Almeida RP, Nascimento FE, Chau J, Prado SS, Tsai CW, Lopes SA, Lopes JR (2008). Genetic structure and biology of //Xylella fastidiosa// | ||
| + | |||
| + | Arrieta-Ortiz ML, Rodríguez-R LM, Pérez-Quintero Á, Poulin L, Díaz AC, Arias Rojas N, Trujillo C, Restrepo Benavides M, Bart R, Boch J, Boureau T, Darrasse A, David P, Dugé de Bernonville T, Fontanilla P, Gagnevin L, Guérin F, Jacques MA, Lauber E, Lefeuvre P, Medina C, Medina E, Montenegro N, Muñoz Bodnar A, Noël LD, Ortiz Quiñones JF, Osorio D, Pardo C, Patil PB, Poussier S, Pruvost O, Robène-Soustrade I, Ryan RP, Tabima J, Urrego Morales OG, Vernière C, Carrere S, Verdier V, Szurek B, Restrepo S, López C, Koebnik R, Bernal A (2013). Genomic survey of pathogenicity determinants and VNTR markers in the cassava bacterial pathogen // | ||
| Bellanger N, Dereeper A, Koebnik R (2022). Clustered regularly interspaced short palindromic repeats in // | Bellanger N, Dereeper A, Koebnik R (2022). Clustered regularly interspaced short palindromic repeats in // | ||
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| Cesbron S, Pothier J, Gironde S, Jacques MA, Manceau C (2014). Development of multilocus variable-number tandem repeat analysis (MLVA) for // | Cesbron S, Pothier J, Gironde S, Jacques MA, Manceau C (2014). Development of multilocus variable-number tandem repeat analysis (MLVA) for // | ||
| + | |||
| + | Coletta-Filho HD, Francisco CS, Lopes JR, Muller C, Almeida RP (2017). Homologous recombination and //Xylella fastidiosa// | ||
| Coletta-Filho HD, Machado MA (2002). Evaluation of the genetic structure of //Xylella fastidiosa// | Coletta-Filho HD, Machado MA (2002). Evaluation of the genetic structure of //Xylella fastidiosa// | ||
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| Ibrahim YE, Widyawan A, Olivier P, Sharafaddin AH, Karine B, Al‐Saleh MA (2023). Characterization of // | Ibrahim YE, Widyawan A, Olivier P, Sharafaddin AH, Karine B, Al‐Saleh MA (2023). Characterization of // | ||
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| + | Jacques MA, Denancé N, Legendre B, Morel E, Briand M, Mississipi S, Durand K, Olivier V, Portier P, Poliakoff F, Crouzillat D (2015). New coffee plant-infecting //Xylella fastidiosa// | ||
| Jeong K, Muñoz-Bodnar A, Arias Rojas N, Poulin L, Rodriguez-R LM, Gagnevin L, Vernière C, Pruvost O, Koebnik R (2019). CRISPR elements provide a new framework for the genealogy of the citrus canker pathogen // | Jeong K, Muñoz-Bodnar A, Arias Rojas N, Poulin L, Rodriguez-R LM, Gagnevin L, Vernière C, Pruvost O, Koebnik R (2019). CRISPR elements provide a new framework for the genealogy of the citrus canker pathogen // | ||
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| + | Kahn AK, Almeida RPP (2022). Phylogenetics of historical host switches in a bacterial plant pathogen. Appl. Environ. Microbiol. 88: e0235621. DOI: [[https:// | ||
| Khojasteh M, Taghavi SM, Khodaygan P, Hamzehzarghani H, Chen G, Bragard C, Koebnik R, Osdaghi E (2019). Molecular typing reveals high genetic diversity of // | Khojasteh M, Taghavi SM, Khodaygan P, Hamzehzarghani H, Chen G, Bragard C, Koebnik R, Osdaghi E (2019). Molecular typing reveals high genetic diversity of // | ||
| Khoodoo MHR, Jaufeerally-Fakim Y (2004). RAPD-PCR fingerprinting and Southern analysis of // | Khoodoo MHR, Jaufeerally-Fakim Y (2004). RAPD-PCR fingerprinting and Southern analysis of // | ||
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| + | Landa BB, Castillo AI, Giampetruzzi A, Kahn A, Román-Écija M, Velasco-Amo MP, Navas-Cortés JA, Marco-Noales E, Barbé S, Moralejo E, Coletta-Filho HD, Saldarelli P, Saponari M, Almeida RPP (2020). Emergence of a plant pathogen in Europe associated with multiple intercontinental introductions. Appl. Environ. Microbiol. 86: e01521-19. DOI: [[https:// | ||
| Leduc A, Traoré YN, Boyer K, Magne M, Grygiel P, Juhasz CC, Boyer C, Guerin F, Wonni I, Ouedraogo L, Vernière C, Ravigné V, Pruvost O (2015). Bridgehead invasion of a monomorphic plant pathogenic bacterium: // | Leduc A, Traoré YN, Boyer K, Magne M, Grygiel P, Juhasz CC, Boyer C, Guerin F, Wonni I, Ouedraogo L, Vernière C, Ravigné V, Pruvost O (2015). Bridgehead invasion of a monomorphic plant pathogenic bacterium: // | ||
| Loreti S, Gallelli A, Belisario A, Wajnberg E, Corazza L (2001). Investigation of genomic variability of // | Loreti S, Gallelli A, Belisario A, Wajnberg E, Corazza L (2001). Investigation of genomic variability of // | ||
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| + | Marcelletti S, Scortichini M (2016). Genome-wide comparison and taxonomic relatedness of multiple //Xylella fastidiosa// | ||
| Martins PMM, Granato LM, Morgan T, Nalin JL, Takita MA, Alfenas-Zerbini P, de Souza AA (2024). Analysis of CRISPR-Cas loci distribution in // | Martins PMM, Granato LM, Morgan T, Nalin JL, Takita MA, Alfenas-Zerbini P, de Souza AA (2024). Analysis of CRISPR-Cas loci distribution in // | ||
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| Montero-Astúa M, Hartung JS, Aguilar E, Chacón C, Li W, Albertazzi FJ, Rivera C (2007). Genetic diversity of //Xylella fastidiosa// | Montero-Astúa M, Hartung JS, Aguilar E, Chacón C, Li W, Albertazzi FJ, Rivera C (2007). Genetic diversity of //Xylella fastidiosa// | ||
| + | |||
| + | Nunney L, Hopkins DL, Morano LD, Russell SE, Stouthamer R (2014a). Intersubspecific recombination in //Xylella fastidiosa// | ||
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| + | Nunney L, Ortiz B, Russell SA, Ruiz Sánchez R, Stouthamer R (2014b). The complex biogeography of the plant pathogen //Xylella fastidiosa//: | ||
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| + | Nunney L, Vickerman DB, Bromley RE, Russell SA, Hartman JR, Morano LD, Stouthamer R (2013). Recent evolutionary radiation and host plant specialization in the //Xylella fastidiosa// | ||
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| + | Nunney L, Yuan X, Bromley RE, Stouthamer R (2012). Detecting genetic introgression: | ||
| Okoh EB, Payne M, Lan R, Riegler M, Chapman T, Bogema D (2024). A multilocus sequence typing scheme for rapid identification of // | Okoh EB, Payne M, Lan R, Riegler M, Chapman T, Bogema D (2024). A multilocus sequence typing scheme for rapid identification of // | ||
| < | < | ||
| + | |||
| + | Parker JK, Havird JC, De La Fuente L (2012). Differentiation of //Xylella fastidiosa// | ||
| Picard Y, Roumagnac P, Legrand D, Humeau L, Robène-Soustrade I, Chiroleu F, Gagnevin L, Pruvost O (2008). Polyphasic characterization of// Xanthomonas axonopodis// | Picard Y, Roumagnac P, Legrand D, Humeau L, Robène-Soustrade I, Chiroleu F, Gagnevin L, Pruvost O (2008). Polyphasic characterization of// Xanthomonas axonopodis// | ||
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| Pruvost O, Richard D, Boyer K, Javegny S, Boyer C, Chiroleu F, Grygiel P, Parvedy E, Robène I, Maillot-Lebon V, Hamza A, Lobin KK, Naiken M, Vernière C (2021). Diversity and geographical structure of // | Pruvost O, Richard D, Boyer K, Javegny S, Boyer C, Chiroleu F, Grygiel P, Parvedy E, Robène I, Maillot-Lebon V, Hamza A, Lobin KK, Naiken M, Vernière C (2021). Diversity and geographical structure of // | ||
| + | |||
| + | Rache L, Blondin L, Diaz Tatis P, Flores C, Camargo A, Kante M, Wonni I, López C, Szurek B, Dupas S, Pruvost O, Koebnik R, Restrepo S, Bernal A, Vernière C (2023). A minisatellite-based MLVA for deciphering the global epidemiology of the bacterial cassava pathogen // | ||
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| + | Rache L, Blondin L, Flores C, Trujillo C, Szurek B, Restrepo S, Koebnik R, Bernal A, Vernière C (2019). An optimized microsatellite scheme for assessing populations of // | ||
| Rademaker JL, Norman DJ, Forster RL, Louws FJ, Schultz MH, de Bruijn FJ (2006). Classification and identification of // | Rademaker JL, Norman DJ, Forster RL, Louws FJ, Schultz MH, de Bruijn FJ (2006). Classification and identification of // | ||
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| Sakthivel K, Kumar A, Gautam RK, Manigundan K, Laha GS, Velazhahan R, Singh R, Yadav IS (2021). Intra-regional diversity of rice bacterial blight pathogen, // | Sakthivel K, Kumar A, Gautam RK, Manigundan K, Laha GS, Velazhahan R, Singh R, Yadav IS (2021). Intra-regional diversity of rice bacterial blight pathogen, // | ||
| + | |||
| + | Scally M, Schuenzel EL, Stouthamer R, Nunney L (2005). Multilocus sequence type system for the plant pathogen //Xylella fastidiosa// | ||
| Scortichini M, Marchesi U, Di Prospero P (2001). Genetic diversity of // | Scortichini M, Marchesi U, Di Prospero P (2001). Genetic diversity of // | ||
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| + | Siddique F, Xiaofeng X, Zhe N, Mingxiu Y, Dawei L, Yuting L, Naibo Y, Younis H, Niaz N, Junhua Z (2025). Genetic diversity and population structure of phyllosphere-associated // | ||
| Timilsina S, Jibrin MO, Potnis N, Minsavage GV, Kebede M, Schwartz A, Bart R, Staskawicz B, Boyer C, Vallad GE, Pruvost O, Jones JB, Goss EM (2015). Multilocus sequence analysis of xanthomonads causing bacterial spot of tomato and pepper plants reveals strains generated by recombination among species and recent global spread of // | Timilsina S, Jibrin MO, Potnis N, Minsavage GV, Kebede M, Schwartz A, Bart R, Staskawicz B, Boyer C, Vallad GE, Pruvost O, Jones JB, Goss EM (2015). Multilocus sequence analysis of xanthomonads causing bacterial spot of tomato and pepper plants reveals strains generated by recombination among species and recent global spread of // | ||
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| + | Trujillo CA, Arias-Rojas N, Poulin L, Medina CA, Tapiero A, Restrepo S, Koebnik R, Bernal AJ (2014). Population typing of the causal agent of cassava bacterial blight in the Eastern Plains of Colombia using two types of molecular markers. BMC Microbiol. 14: 161. DOI: [[https:// | ||
| Vancheva T, Bogatzevska N, Moncheva P, Mitrev S, Vernière C, Koebnik R (2021). Molecular epidemiology of // | Vancheva T, Bogatzevska N, Moncheva P, Mitrev S, Vernière C, Koebnik R (2021). Molecular epidemiology of // | ||
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| + | Vancheva T, Stoyanova M, Tasheva-Terzieva E, Bogatzevska N, Moncheva P (2018). Molecular methods for diversity assessment among xanthomonads of Bulgarian and Macedonian pepper. Braz. J. Microbiol. 49: 246-259. DOI: [[https:// | ||
| Vernière C, Bui Thi Ngoc L, Jarne P, Ravigné V, Guérin F, Gagnevin L, Le Mai N, Chau NM, Pruvost O (2014). Highly polymorphic markers reveal the establishment of an invasive lineage of the citrus bacterial pathogen // | Vernière C, Bui Thi Ngoc L, Jarne P, Ravigné V, Guérin F, Gagnevin L, Le Mai N, Chau NM, Pruvost O (2014). Highly polymorphic markers reveal the establishment of an invasive lineage of the citrus bacterial pathogen // | ||
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| Wonni I, Cottyn B, Detemmerman L, Dao S, Ouedraogo L, Sarra S, Tekete C, Poussier S, Corral R, Triplett L, Koita O, Koebnik R, Leach J, Szurek B, Maes M, Verdier V (2014). Analysis of // | Wonni I, Cottyn B, Detemmerman L, Dao S, Ouedraogo L, Sarra S, Tekete C, Poussier S, Corral R, Triplett L, Koita O, Koebnik R, Leach J, Szurek B, Maes M, Verdier V (2014). Analysis of // | ||
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| + | Yuan X, Morano L, Bromley R, Spring-Pearson S, Stouthamer R, Nunney L (2010). Multilocus sequence typing of //Xylella fastidiosa// | ||
| Zhao S, Poulin L, Rodriguez-R LM, Serna NF, Liu SY, Wonni I, Szurek B, Verdier V, Leach JE, He YQ, Feng JX, Koebnik R (2012). Development of a variable number of tandem repeats typing scheme for the bacterial rice pathogen // | Zhao S, Poulin L, Rodriguez-R LM, Serna NF, Liu SY, Wonni I, Szurek B, Verdier V, Leach JE, He YQ, Feng JX, Koebnik R (2012). Development of a variable number of tandem repeats typing scheme for the bacterial rice pathogen // | ||
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| Baldi P, La Porta N (2017). //Xylella fastidiosa//: | Baldi P, La Porta N (2017). //Xylella fastidiosa//: | ||
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| + | Nunney L, Elfekih S, Stouthamer R (2012). The importance of multilocus sequence typing: cautionary tales from the bacterium //Xylella fastidiosa// | ||
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typing/molecular_typing.1739457009.txt.gz · Last modified: 2025/02/13 14:30 by rkoebnik
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