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Molecular Diagnosis and Diversity for Regulated Xanthomonas


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typing:molecular_typing

Taxonomy and Diversity of Xanthomonads

This data is based on the review by Catara (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.

Tools for molecular typing of regulated Xanthomonas

Pathogen Fingerprints VNTR/MLVA CRISPR MLSA/MLST
A1 list
X. citri pv. aurantifolii NA1 NA NA Mhedbi-Hajri (2013)
X. citri pv. citri Bui Thi Ngoc (2010),
Escalon (2013)
Bui Thi Ngoc (2009),
Pruvost (2015),
Leduc (2015),
Pruvost (2019),
Pruvost (2021)
Jeong (2019) Bui Thi Ngoc (2010),
Mhedbi-Hajri (2013)
X. euvesicatoria pv. allii Gent (2004),
Gent (2005),
Humeau (2006),
Picard(2008)
Vancheva (2021) NA Mhedbi-Hajri (2013)
X. oryzae pv. oryzae George (1997) Poulin (2015) NA Hajri (2012),
Wonni (2014),
Sakthivel (2021)
X. oryzae pv. oryzicola NA Zhao (2012),
Poulin (2015)
NA Hajri (2012),
Zhao (2012)
A2 list
X. arboricola pv. corylina NA Cesbron (2014),
Essakhi (2015)
NA Essakhi (2015)
X. arboricola pv. juglandis Loreti (2001),
Scortichini (2001),
Hajri (2010)
Essakhi (2015) NA Essakhi (2015)
X. arboricola pv. pruni Boudon (2005) Scortichini (2001),
Essakhi (2015)
NA Boudon (2005),
Essakhi (2015)
X. axonopodis pv. poinsettiicola NA NA NA Rockey (2015)
X. euvesicatoria pv. euvesicatoria Hamza (2010),
Hamza (2012)
Vancheva (2021) NA Hamza (2010),
Hamza (2012),
Mhedbi-Hajri (2013),
Dhakal (2019)
X. euvesicatoria pv. perforans Hamza (2010),
Hamza (2012)
Vancheva (2021) NA Hamza (2010),
Hamza (2012)
X. fragariae Pooler (1996),
Roberts (1998)
Gétaz (2018) Gétaz (2018) Gétaz (2018)
X. hortorum pv. gardneri Hamza (2010),
Hamza (2012)
NA NA Hamza (2010),
Hamza (2012)
X. phaseoli pv. dieffenbachiae Khoodoo (2004),
Donahoo (2013)
NA NA Mhedbi-Hajri (2013)
X. phaseoli pv. phaseoli, X. citri pv. fuscans Mkandawire (2004) NA NA Mhedbi-Hajri (2013)
X. translucens pv. translucens Bragard (1997),
Rademaker (2006)
NA NA Curland (2018),
Khojasteh (2019),
Curland (2020
X. vesicatoria Hamza (2010),
Hamza (2012)
NA NA Hamza (2010),
Hamza (2012),
Dhakal (2019)

1 NA: not available.

References

Boudon S, Manceau C, Nottéghem JL (2005). Structure and origin of Xanthomonas arboricola pv. pruni populations causing bacterial spot of stone fruit trees in Western Europe. Phytopathology 95: 1081-1088. DOI: 10.1094/PHYTO-95-1081

Bragard C, Singer E, Alizadeh A, Vauterin L, Maraite H, Swings J (1997). Xanthomonas translucens from small grains: diversity and phytopathological relevance. Phytopathology 87: 1111-1117. DOI: 10.1094/PHYTO.1997.87.11.1111

Bui Thi Ngoc L, Vernière C, Jouen E, Ah-You N, Lefeuvre P, Chiroleu F, Gagnevin L, Pruvost O. (2010). Amplified fragment length polymorphism and multilocus sequence analysis-based genotypic relatedness among pathogenic variants of Xanthomonas citri pv. citri and Xanthomonas campestris pv. bilvae. Int. J. Syst. Evol. Microbiol. 60: 515-525. DOI: 10.1099/ijs.0.009514-0

Bui Thi Ngoc L, Verniere C, Vital K, Guerin F, Gagnevin L, Brisse S, Ah-You N, Pruvost O (2009). Development of 14 minisatellite markers for the citrus canker bacterium, Xanthomonas citri pv. citri. Mol. Ecol. Resour. 9: 125-127. DOI: 10.1111/j.1755-0998.2008.02242.x

Cesbron S, Pothier J, Gironde S, Jacques MA, Manceau C (2014). Development of multilocus variable-number tandem repeat analysis (MLVA) for Xanthomonas arboricola pathovars. J. Microbiol. Methods 100: 84-90. DOI: 10.1016/j.mimet.2014.02.017

Curland RD, Gao L, Bull CT, Vinatzer BA, Dill-Macky R, Van Eck L, Ishimaru CA (2018). Genetic diversity and virulence of wheat and barley strains of Xanthomonas translucens from the Upper Midwestern United States. Phytopathology 108: 443-453. DOI: 10.1094/PHYTO-08-17-0271-R

Curland RD, Gao L, Hirsch CD, Ishimaru CA (2020). Localized genetic and phenotypic diversity of Xanthomonas translucens associated with bacterial leaf streak on wheat and barley in Minnesota. Phytopathology 110: 257-266. DOI: 10.1094/PHYTO-04-19-0134-R

Dhakal U, Dobhal S, Alvarez AM, Arif M (2019). Phylogenetic analyses of xanthomonads causing bacterial leaf spot of tomato and pepper: Xanthomonas euvesicatoria revealed homologous populations despite distant geographical distribution. Microorganisms 7: 462. DOI: 10.3390/microorganisms7100462

Donahoo RS, Jones JB, Lacy GH, Stromberg VK, Norman DJ (2013). Genetic analyses of Xanthomonas axonopodis pv. dieffenbachiae strains reveal distinct phylogenetic groups. Phytopathology 103: 237-244. DOI: 10.1094/PHYTO-08-12-0191-R

Escalon A, Javegny S, Vernière C, Noël LD, Vital K, Poussier S, Hajri A, Boureau T, Pruvost O, Arlat M, Gagnevin L (2013). Variations in type III effector repertoires, pathological phenotypes and host range of Xanthomonas citri pv. citri pathotypes. Mol. Plant Pathol. 14: 483-496. DOI: 10.1111/mpp.12019

Essakhi S, Cesbron S, Fischer-Le Saux M, Bonneau S, Jacques MA, Manceau C (2015). Phylogenetic and variable-number tandem-repeat analyses identify nonpathogenic Xanthomonas arboricola lineages lacking the canonical type III secretion system. Appl. Environ. Microbiol. 81: 5395-5410. DOI: 10.1128/AEM.00835-15

Gent DH, Al-Saadi A, Gabriel DW, Louws FJ, Ishimaru CA, Schwartz HF (2005). Pathogenic and genetic relatedness among Xanthomonas axonopodis pv. allii and other pathovars of X. axonopodis. Phytopathology 95: 918-925. DOI: 10.1094/PHYTO-95-0918

Gent DH, Schwartz HF, Ishimaru CA, Louws FJ, Cramer RA, Lawrence CB (2004). Polyphasic characterization of Xanthomonas strains from onion. Phytopathology 94: 184-195. DOI: 10.1094/PHYTO.2004.94.2.184

George ML, Bustamam M, Cruz WT, Leach JE, Nelson RJ (1997). Movement of Xanthomonas oryzae pv. oryzae in Southeast Asia detected using PCR-based DNA fingerprinting. Phytopathology 87: 302-309. DOI: 10.1094/PHYTO.1997.87.3.302

Gétaz M, Krijger M, Rezzonico F, Smits THM, van der Wolf JM, Pothier JF (2018). Genome-based population structure analysis of the strawberry plant pathogen Xanthomonas fragariae reveals two distinct groups that evolved independently before its species description. Microb. Genom. 4: e000189. DOI: 10.1099/mgen.0.000189

Hajri A, Brin C, Zhao S, David P, Feng JX, Koebnik R, Szurek B, Verdier V, Boureau T, Poussier S (2012). Multilocus sequence analysis and type III effector repertoire mining provide new insights into the evolutionary history and virulence of Xanthomonas oryzae. Mol. Plant Pathol. 13: 288-302. DOI: 10.1111/j.1364-3703.2011.00745.x

Hajri A, Meyer D, Delort F, Guillaumès J, Brin C, Manceau C (2010). Identification of a genetic lineage within Xanthomonas arboricola pv. juglandis as the causal agent of vertical oozing canker of Persian (English) walnut in France. Plant Pathol. 59: 1014-1022. DOI: 10.1111/j.1365-3059.2010.02362.x

Hamza AA, Robène-Soustrade I, Jouen E, Gagnevin L, Lefeuvre P, Chiroleu F, Pruvost O (2010). Genetic and pathological diversity among Xanthomonas strains responsible for bacterial spot on tomato and pepper in the Southwest Indian Ocean Region. Plant Dis. 94: 993-999. DOI: 10.1094/PDIS-94-8-0993

Hamza AA, Robene-Soustrade I, Jouen E, Lefeuvre P, Chiroleu F, Fisher-Le Saux M, Gagnevin L, Pruvost O (2012). MultiLocus Sequence Analysis- and Amplified Fragment Length Polymorphism-based characterization of xanthomonads associated with bacterial spot of tomato and pepper and their relatedness to Xanthomonas species. Syst. Appl. Microbiol. 35: 183-190. DOI: 10.1016/j.syapm.2011.12.005

Humeau L, Roumagnac P, Picard Y, Robène-Soustrade I, Chiroleu F, Gagnevin L, Pruvost O (2006). Quantitative and molecular epidemiology of bacterial blight of onion in seed production fields. Phytopathology 96: 1345-1354. DOI: 10.1094/PHYTO-96-1345

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 Xanthomonas citri pv. citri. BMC Genomics 20: 917. DOI: 10.1186/s12864-019-6267-z

Khojasteh M, Taghavi SM, Khodaygan P, Hamzehzarghani H, Chen G, Bragard C, Koebnik R, Osdaghi E (2019). Molecular typing reveals high genetic diversity of Xanthomonas translucens strains infecting small-grain cereals in Iran. Appl. Environ. Microbiol. 85: e01518-19. DOI: 10.1128/AEM.01518-19

Khoodoo MHR, Jaufeerally-Fakim Y (2004). RAPD-PCR fingerprinting and Southern analysis of Xanthomonas axonopodis pv. dieffenbachiae strains isolated from different aroid hosts and locations. Plant Dis. 88: 980-988. DOI: 10.1094/PDIS.2004.88.9.980

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: Xanthomonas citri pv. citri, an emerging citrus pathogen in Mali and Burkina Faso. Environ. Microbiol. 17: 4429-4442. DOI: 10.1111/1462-2920.12876

Loreti S, Gallelli A, Belisario A, Wajnberg E, Corazza L (2001). Investigation of genomic variability of Xanthomonas arboricola pv. juglandis by AFLP analysis. Eur. J. Plant Pathol. 107: 583-591. DOI:10.1023/A:1017951406237

Mhedbi-Hajri N, Hajri A, Boureau T, Darrasse A, Durand K, Brin C, Fischer-Le Saux M, Manceau C, Poussier S, Pruvost O, Lemaire C, Jacques MA (2013). Evolutionary history of the plant pathogenic bacterium Xanthomonas axonopodis. PLoS One 8: e58474. DOI: 10.1371/journal.pone.0058474

Mkandawire AB, Mabagala RB, Guzmán P, Gepts P, Gilbertson RL (2004). Genetic diversity and pathogenic variation of common blight bacteria (Xanthomonas campestris pv. phaseoli and X. campestris pv. phaseoli var. fuscans) suggests pathogen coevolution with the common bean. Phytopathology 94: 593-603. DOI: 10.1094/PHYTO.2004.94.6.593

Picard Y, Roumagnac P, Legrand D, Humeau L, Robène-Soustrade I, Chiroleu F, Gagnevin L, Pruvost O (2008). Polyphasic characterization of Xanthomonas axonopodis pv. allii associated with outbreaks of bacterial blight on three Allium species in the Mascarene archipelago. Phytopathology 98: 919-925. DOI: 10.1094/PHYTO-98-8-0919

Pooler MR, Ritchie DF, Hartung JS (1996). Genetic relationships among strains of Xanthomonas fragariae based on random amplified polymorphic DNA PCR, repetitive extragenic palindromic PCR, and enterobacterial repetitive intergenic consensus PCR data and generation of multiplexed PCR primers useful for the identification of this phytopathogen. Appl. Environ. Microbiol. 62: 3121-3127. DOI: 10.1128/aem.62.9.3121-3127.1996

Poulin L, Grygiel P, Magne M, Gagnevin L, Rodriguez-R LM, Forero Serna N, Zhao S, El Rafii M, Dao S, Tekete C, Wonni I, Koita O, Pruvost O, Verdier V, Vernière C, Koebnik R (2015). New multilocus variable-number tandem-repeat analysis tool for surveillance and local epidemiology of bacterial leaf blight and bacterial leaf streak of rice caused by Xanthomonas oryzae. Appl. Environ. Microbiol. 81: 688-698. DOI: 10.1128/AEM.02768-14

Pruvost O, Boyer K, Ravigné V, Richard D, Vernière C (2019). Deciphering how plant pathogenic bacteria disperse and meet: Molecular epidemiology of Xanthomonas citri pv. citri at microgeographic scales in a tropical area of Asiatic citrus canker endemicity. Evol. Appl. 12: 1523-1538. DOI: 10.1111/eva.12788

Pruvost O, Magne M, Boyer K, Leduc A, Tourterel C, Drevet C, Ravigné V, Gagnevin L, Guérin F, Chiroleu F, Koebnik R, Verdier V, Vernière C (2014). A MLVA genotyping scheme for global surveillance of the citrus pathogen Xanthomonas citri pv. citri suggests a worldwide geographical expansion of a single genetic lineage. PLoS One 9: e98129. DOI: 10.1371/journal.pone.0098129

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 Xanthomonas citri pv. citri on Citrus in the South West Indian Ocean Region. Microorganisms 9: 945. DOI: 10.3390/microorganisms9050945

Rademaker JL, Norman DJ, Forster RL, Louws FJ, Schultz MH, de Bruijn FJ (2006). Classification and identification of Xanthomonas translucens isolates, including those pathogenic to ornamental asparagus. Phytopathology 96: 876-884. DOI: 10.1094/PHYTO-96-0876

Roberts PD, Hodge NC, Bouzar H, Jones JB, Stall RE, Berger RD, Chase AR (1998). Relatedness of strains of Xanthomonas fragariae by restriction fragment length polymorphism, DNA-DNA reassociation, and fatty acid analyses. Appl. Environ. Microbiol. 64: 3961-3965. DOI: 10.1128/AEM.64.10.3961-3965.1998

Rockey W, Potnis N, Timilsina S, Hong JC, Vallad GE, Jones JB, Norman DJ (2015). Multilocus sequence analysis reveals genetic diversity in xanthomonads associated with poinsettia production. Plant Dis. 99: 874-882. DOI: 10.1094/PDIS-08-14-0867-RE

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, Xanthomonas oryzae pv. oryzae, in the Andaman Islands, India: revelation by pathotyping and multilocus sequence typing. J. Appl. Microbiol. 130: 1259-1272. DOI: 10.1111/jam.14813

Scortichini M, Marchesi U, Di Prospero P (2001). Genetic diversity of Xanthomonas arboricola pv. juglandis (synonyms: X. campestris pv. juglandis; X. juglandis pv. juglandis) strains from different geographical areas shown by repetitive polymerase chain reaction genomic fingerprinting. J. Phytopathol. 149: 325-332. DOI: 10.1046/j.1439-0434.2001.00628.x

Vancheva T, Bogatzevska N, Moncheva P, Mitrev S, Vernière C, Koebnik R (2021). Molecular epidemiology of Xanthomonas euvesicatoria strains from the Balkan Peninsula revealed by a new multiple-locus variable-number tandem-repeat analysis scheme. Microorganisms 9: 536. DOI: 10.3390/microorganisms9030536

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 Xanthomonas oryzae pv. oryzicola population in Mali and Burkina Faso reveals a high level of genetic and pathogenic diversity. Phytopathology 104: 520-531. DOI: 10.1094/PHYTO-07-13-0213-R

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 Xanthomonas oryzae pv. oryzicola. Phytopathology 102: 948-956. DOI: 10.1094/PHYTO-04-12-0078-R

Further reading

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

typing/molecular_typing.txt · Last modified: 2022/05/04 19:34 by rkoebnik