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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.
Main protocols described for regulated xanthomonads and beyond based on amplification of specific target DNAs.
1 qPCR: quantitative real-time PCR; 2 IA: isothermal amplification: 3 NA: not applicable.
Aglietti C, Luchi N, Pepori AL, Bartolini P, Pecori F, Raio A, Capretti P, Santini A (2019). Real-time loop-mediated isothermal amplification: an early-warning tool for quarantine plant pathogen detection. AMB Express 9: 50. DOI: 10.1186/s13568-019-0774-9
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 in Mexican vineyards. Plant Dis. 105: 1490-1494. DOI: 10.1094/PDIS-09-20-1900-RE
Amoia SS, Loconsole G, Ligorio A, Pantazis AK, Papadakis G, Gizeli E, Minafra A (2023). A colorimetric LAMP detection of Xylella fastidiosa in crude alkaline sap of olive trees in apulia as a field-based tool for disease containment. Agriculture 13: 448. DOI: 10.3390/agriculture13020448
Araújo ER, Costa JR, Ferreira MASV, Quezado-Duval AM (2012). Simultaneous detection and identification of the Xanthomonas species complex associated with tomato bacterial spot using species-specific primers and multiplex PCR. J. Appl. Microbiol. 113: 1479-1490. DOI: 10.1111/j.1365-2672.2012.05431.x
Araújo ER, Ferreira MASV, Quezado-Duval AM (2013). Specific primers for Xanthomonas vesicatoria, a tomato bacterial spot causal agent. Eur. J. Plant Pathol. 137: 5-9. DOI: 10.1007/s10658-013-0225-4
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Back CG, Lee SY, Lee BJ, Yea MC, Kim SM, Kang IK, Cha JS, Jung HY (2015). Development of a species-specific PCR assay for three Xanthomonas species, causing bulb and flower diseases, based on their genome sequences. Plant Pathol. J. 31: 212-218. DOI: 10.5423/PPJ.OA.04.2015.0049
Beran P, Mráz I (2013). Species-specific PCR primers for detection of Xanthomonas vesicatoria. Crop. Prot. 43: 213-215. DOI: 10.1016/j.cropro.2012.08.008
Beran P, Stehlikova D, Cohen SP, Rost M, Beranova K, Curn V (2023). Utilization of a new hundred-genomes pipeline to design a rapid duplex LAMP detection assay for Xanthomonas euvesicatoria and X. vesicatoria in tomato. Plant Dis. 107: 1822-1828. DOI: 10.1094/PDIS-05-22-1098-RE
Bispo Carvalho IC, Silva Carvalho AM, Wendland A, Rossato M (2024). Colorimetric LAMP assay for detection of Xanthomonas phaseoli pv. manihotis in cassava through genomics: a new approach to an old problem. Plant Dis. 108: 2993-3000. DOI: 10.1094/PDIS-08-23-1507-RE
Buddhachat K, Ritbamrung O, Inthima P, Ratanasut K, Sujipuli K (2024). Rapid detection of two pathogenically important Xanthomonas in rice using a loop-mediated isothermal amplification with lateral flow dipstick (LAMP-LFD). Crop Protection 175: 106466. DOI: 10.1016/j.cropro.2023.106466
Buddhachat K, Ritbamrung O, Sripairoj N, Inthima P, Ratanasut K, Boonsrangsom T, Sujipuli K (2021). One-step colorimetric LAMP (cLAMP) assay for visual detection of Xanthomonas oryzae pv. oryzae in rice. Crop Prot. 150: 105809. DOI: 10.1016/j.cropro.2021.105809
Bühlmann A, Pothier JF, Tomlinson JA, Frey JE, Boonham N, Smits THM, Duffy B (2013). Genomics-informed design of loop-mediated isothermal amplification for detection of phytopathogenic Xanthomonas arboricola pv. pruni at the intraspecific level. Plant Pathol. 62: 475-484. DOI: 10.1111/j.1365-3059.2012.02654.x
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
Chabirand A, Jouen E, Pruvost O, Chiroleu F, Hostachy B, Bergsma-Vlami M, Bianchi G, Cozzolino L, Elphinstone J, Holeva M, Manole F, Martini P, Matoušková H, Minatchy J, Op de Beeck G, Poliakoff F, Sigillo L, Siverio F, Van Vaerenbergh J, Laurentie M, Robène-Soustrade I (2014). Comparative and collaborative studies for the validation of a nested PCR for the detection of Xanthomonas axonopodis pv. dieffenbachiae from Anthurium samples. Plant Pathol. 63: 20-30. DOI: 10.1111/ppa.12083
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Coletta-Filho HD, Takita MA, De Souza AA, Neto JR, Destéfano SAL, Hartung JS, Machado MA (2006). Primers based on the rpf gene region provide improved detection of Xanthomonas axonopodis pv. citri in naturally and artificially infected citrus plants. J. Appl. Microbiol. 100: 279-285. DOI: 10.1111/j.1365-2672.2005.02787.x
Cruz L, Sousa-Santos M (1999). Optimizing PCR technique for large scale diagnosis of angular leaf spot of strawberry in Fragaria plants. Petria 9: 77-80.
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Cubero J, Graham JH (2002). Genetic relationship among worldwide strains of Xanthomonas causing canker in citrus species and design of new primers for their identification by PCR. Appl. Environ. Microbiol. 68: 1257-1264. DOI: 10.1128/AEM.68.3.1257-1264.2002
Cubero J, Graham JH (2005). Quantitative real-time polymerase chain reaction for bacterial enumeration and allelic discrimination to differentiate Xanthomonas strains on citrus. Phytopathology 95: 1333-1340. DOI: 10.1094/PHYTO-95-1333
Cui Z, Ojaghian MR, Tao Z, Kakar KU, Zeng J, Zhao W, Duan Y, Vera Cruz CM, Li B, Zhu B, Xie G (2016). Multiplex PCR assay for simultaneous detection of six major bacterial pathogens of rice. J. Appl. Microbiol.120,1357–1367.DOI: 10.1111/jam.13094
De Paiva BAR, Wendland A, Teixeira NC, Ferreira MASV (2020). Rapid detection of Xanthomonas citripv. fuscans and Xanthomonas phaseoli pv. phaseoli in common bean by Loop-Mediated Isothermal Amplification. Plant Dis. 104: 198-203. DOI: 10.1094/PDIS-02-19-0325-RE
Del Pilar Velasco Amo M, Olivares-García C, Román-Écija M, Marco-Noales E, Navas-Cortés JA, Landa Del Castillo BB (2025). Modeling the accuracy of Xylella fastidiosa molecular diagnostic tests in naturally-infected almond tree samples. Plant Dis., in press. DOI: 10.1094/PDIS-12-24-2568-RE
Dupas E, Legendre B, Olivier V, Poliakoff F, Manceau C, Cunty A (2019). Comparison of real-time PCR and droplet digital PCR for the detection of Xylella fastidiosa in plants. J. Microbiol. Methods 162: 86-95. DOI: 10.1016/j.mimet.2019.05.010
Ejaz K, Faiq A, Asif M, Zaka A, Nguyen MH, Cruz CV, Oliva R, Arif M, Yasmin S (2022) Molecular characterization and screening of Xanthomonas oryzae pv. oryzae, isolated from Pakistan for prediction of bacterial leaf blight-resistant basmati rice. Physiol. Mol. Plant Pathol. 121: 101858. DOI: 10.1016/j.pmpp.2022.101858
Elbeaino T, Incerti O, Dakroub H, Valentini F, Huang Q (2020). Development of an FTP-LAMP assay based on TaqMan real-time PCR and LAMP for the specific detection of Xylella fastidiosa De Donno and mulberry strains in both plants and insect vectors. J. Microbiol. Methods 175: 105992. DOI: 10.1016/j.mimet.2020.105992
Farrall T, Abeynayake SW, Webster W, Fiorito S, Dinsdale A, Whattam M, Campbell PR, Gambley C (2024). Development of a rapid, accurate, and field deployable LAMP-CRISPR-Cas12a integrated assay for Xylella fastidiosa detection and surveillance. Australas. Plant Pathol. 53: 115-120. DOI: 10.1007/s13313-023-00954-4
Fernandes C, Albuquerque P, Sousa R, Cruz L, Tavares F (2017). Multiple DNA markers for identification of Xanthomonas arboricola pv. juglandis isolates and its direct detection in plant samples. Plant Dis. 101: 858-865. DOI: 10.1094/PDIS-10-16-1481-RE
Fonseca, NP, Felestrino ÉB, Caneschi WL, Sanchez AB, CordeiroIF, Lemes CGC, Assis RAB, Carvalho FMS, Ferro JA, Varani AM, Belasque J, Setubal JC, Telles GP, Aguena DS, Almeida NF, Moreira LM (2019). Detection and identification of Xanthomonas pathotypes associated with citrus diseases using comparative genomics and multiplex PCR. PeerJ 7: e7676. DOI: 10.7717/peerj.7676
Fu H, Fleitas MC, Sarkes A, Wang L, Yang Y, Zahr K, Harding MW, Feindel D, Kutcher R, Feng J (2024). Detection and differentiation of Xanthomonas translucens pathovars translucens and undulosa from wheat and barley by duplex quantitative PCR. Plant Dis. 108: 270-277. DOI: 10.1094/PDIS-05-23-0887-SR
Garita-Cambronero J, Palacio-Bielsa A, López MM, Cubero J (2017). Pan-genomic analysis permits differentiation of virulent and non-virulent strains of Xanthomonas arboricola that cohabit Prunus spp. and elucidate bacterial virulence factors. Front. Microbiol. 8: 573. DOI: 10.3389/fmicb.2017.00573
Gétaz M, Bühlmann A, Schneeberger PHH, Van Malderghem C, Duffy B, Maes M, Pothier JF, Cottyn B (2017). A diagnostic tool for improved detection of Xanthomonas fragariae using a rapid and highly specific LAMP assay designed with comparative genomics. Plant Pathol. 66: 1094-1102. DOI: 10.1111/ppa.12665
Harper SJ, Ward LI, Clover GR (2010). Development of LAMP and real-time PCR methods for the rapid detection of Xylella fastidiosa for quarantine and field applications. Phytopathology 100: 1282-1288. DOI: 10.1094/PHYTO-06-10-0168
Hartung J, Pruvost OP, Villemot I, Alvarez A (1996). Rapid and sensitive colorimetric detection of Xanthomonas axonopodis pv. citri by immunocapture and a nested polymerase chain reaction assay. Phytopathology 86: 95. DOI: 10.1094/Phyto-86-95
Hartung JS, Pooler MR (1997). Immunocapture and multiplexed-PCR assay for Xanthomonas fragariae, causal agent of angular leafspot disease. Int. Soc. Hortic. Sci. 439: 821-828. DOI: 10.17660/ActaHortic.1997.439.136
Hill RS, Pal A, Dewdney MM, Cano L, Harmon CL (2025). Development and validation of an RPA assay for detecting Xanthomonas citri subsp. citri A, A*, and Aw and X. fuscans subsp. aurantifolii B and C. PhytoFrontiers 5: 197-208. DOI: 10.1094/PHYTOFR-10-24-0120-FI
Hodgetts J (2022). A panel of real-time PCR assays for the direct detection of all of the Xylella fastidiosa subspecies. Methods Mol. Biol. 2536: 201-230. DOI: 10.1007/978-1-0716-2517-0_13
Hodgetts J, Glover R, Cole J, Hall J, Boonham N (2021). Genomics informed design of a suite of real-time PCR assays for the specific detection of each Xylella fastidiosa subspecies. J. Appl. Microbiol. 131: 855-872. DOI: 10.1111/jam.14903
Hong E, Bankole I, Zhao B, Shi G, Buck J, Feng J, Curland RD, Baldwin TT, Chapara VR, Liu Z (2023). DNA markers, pathogenicity test and multilocus sequence analysis to differentiate and characterize cereal specific Xanthomonas translucens strains. Phytopathology 113: 2062-2072. DOI: 10.1094/PHYTO-10-22-0381-SA
Immanuel T, Taylor R, Keeling S, Brosnahan C, Alexander B (2020). Discrimination between viable and dead Xanthomonas fragariae in strawberry using viability PCR. J. Phytopathol. 168: 363-373. DOI: 10.1111/jph.12900
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 variants derived via homologous recombination. Appl. Environ. Microbiol. 82: 1556-1568. DOI: 10.1128/AEM.03299-15
Jouen E, Chiroleu F, Maillot-Lebon V, Chabirand A, Merion S, Boyer C, Pruvost O, Robène I (2019). A duplex quantitative real-time PCR assay for the detection and quantification of Xanthomonas phaseoli pv. dieffenbachiae from diseased and latently infected anthurium tissue. J. Microbiol. Methods 161: 74-83. DOI: j.mimet.2019.03.003
Jun-Hai N, Yue-Rong G, Jun-Mei Y, Qing-Yun L, Guang-Sui Y, Cun W, Yu R (2015). Development and evaluation of a loop-mediated isothermal amplification assay for rapid detection of bacterial blight pathogen (Xanthomonas axonopodis pv. dieffenbachiae) in anthurium. Eur. J. Plant Pathol. 142: 801-813. DOI: 10.1007/s10658-015-0653-4
Kałużna M, Prokić A, Obradović A, Weldon WA, Stockwell VO, Pothier JF (2023). Specific and sensitive detection tools for Xanthomonas arboricola pv. corylina, the causal agent of bacterial blight of hazelnut, developed with comparative genomics. Front. Plant Sci. 14: 1254107. DOI: 10.3389/fpls.2023.1254107
Kang MJ, Kim MH, Hwang DJ, Cho MS, Seol Y, Hahn JH, Ryu S, Park DS (2012). Quantitative in planta PCR assay for specific detection of Xanthomonas oryzae pv. oryzicola using putative membrane protein based primer set. Crop. Prot. 40: 22-27. DOI: 10.1016/j.cropro.2012.04.014
Kang MJ, Shim JK, Cho MS, Seol YJ, Hahn JH, Hwang DJ, Park DS (2008). Specific detection of Xanthomonas oryzae pv. oryzicola in infected rice plant by use of PCR assay targeting a membrane fusion protein gene. J. Microbiol. Biotechnol. 18: 1492-1495. PMID: 18852502
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Koroleva ML, Blinova SA, Shvartsev AA, Kurochkin VE, Alekseev YI (2022). Molecular genetic detection and differentiation of Xanthomonas oryzae pv. oryzicola, bacterial leaf streak agents of rice. Vavilovskii Zhurnal Genet. Selektsii. 26: 544-552. DOI: 10.18699/VJGB-22-66
Kositcharoenkul N, Chatchawankanphanich O, Bhunchoth A, Kositratana W (2011). Detection of Xanthomonas citri subsp. citri from field samples using single-tube nested PCR. Plant Pathol. 60: 436-442. DOI: 10.1111/j.1365-3059.2010.02390.x
Lang JM, Hamilton JP, Diaz MGQ, Van Sluys MA, Burgos MRG, Vera Cruz CM, Buell CR, Tisserat NA, Leach JE (2010). Genomics-based diagnostic marker development for Xanthomonas oryzae pv. oryzae and X. oryzae pv. oryzicola. Plant Dis. 94: 311-319. DOI: 10.1094/PDIS-94-3-0311
Lang JM, Langlois P, Nguyen MHR, Triplett LR, Purdie L, Holton TA, Djikeng A, Vera Cruz CM, Verdier V, Leach JE (2014). Sensitive detection of Xanthomonas oryzae pathovars oryzae and oryzicolaby loop-mediated isothermal amplification. Appl. Environ. Microbiol. 80: 4519-4530. DOI: 10.1128/AEM.00274-14
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Li W, Lee SY, Back CG, Ten LN, Jung HY (2019). Loop-mediated isothermal amplification for the detection of Xanthomonas arboricola pv. pruni in peaches. Plant Pathol. J. 35: 635-643. DOI: 10.5423/PPJ.OA.07.2019.0197
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