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diagnostics:dna_protocols [2022/05/04 19:33] rkoebnik [Further reading] |
diagnostics:dna_protocols [2022/08/12 17:21] (current) rkoebnik [Table] |
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**Main protocols described for regulated xanthomonads based on amplification of specific target DNAs.** | **Main protocols described for regulated xanthomonads based on amplification of specific target DNAs.** | ||
- | ^ Disease | + | ^ Disease |
- | |Onion bacterial blight |//X. euvesicatoria// | + | | Onion bacterial blight |
- | |Citrus bacterial canker |//X. citri// pv. //citri// \\ //X. aurantifolii// | + | | Citrus bacterial canker |
- | |Bacterial spot of stone fruits, walnut blight, hazelnut blight |//X. arboricola// | + | | Bacterial spot of stone fruits, walnut blight, hazelnut blight |
- | |Bacterial leaf blight and bacterial leaf streak of rice |//X. oryzae// pvs. //oryzae// and // | + | | Bacterial leaf blight and bacterial leaf streak of rice |
- | |Bacterial spot of tomato and sweet pepper |//X. euvesicatoria// | + | | Bacterial spot of tomato and sweet pepper |
- | |Bacterial angular leaf spot of strawberry |//X. fragariae// | + | | Bacterial angular leaf spot of strawberry |
- | |Bacterial blight of anthurium and other aroids |//X. phaseoli// pv. // | + | | Bacterial blight of anthurium and other aroids |
- | |Bacterial leaf spot of poinsettia |//X. axonopodis// | + | | Bacterial leaf spot of poinsettia |
- | |Bacterial leaf streak |//X. translucens// | + | | Bacterial leaf streak |
- | |Common blight of bean |//X. phaseoli// pv. phaseoli, \\ //X. citri// pv. // | + | | Common blight of bean |
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===== References ===== | ===== References ===== | ||
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- | Araújo ER, Ferreira MASV, Quezado-Duval AM (2013) Specific primers for // | + | Araújo ER, Ferreira MASV, Quezado-Duval AM (2013). Specific primers for // |
- | Audy P (1996) A rapid and sensitive PCR-based assay for concurrent detection of bacteria causing common and halo blights in bean seed. Phytopathology 86: 361-366. DOI: [[https:// | + | Audy P, Braat CE, Saindon G, Huang HC, Laroche A (1996). A rapid and sensitive PCR-based assay for concurrent detection of bacteria causing common and halo blights in bean seed. Phytopathology 86: 361-366. DOI: [[https:// |
- | 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 // | + | 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 // |
- | Beran P, Mráz I (2013) Species-specific PCR primers for detection of // | + | Beran P, Mráz I (2013). Species-specific PCR primers for detection of // |
- | 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 // | + | 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 // |
- | Chabirand A, Jouen E, Pruvost O, Chiroleu F, Hostachy B, Bergsma-Vlami M, Bianchi G, Cozzolino L, Elphinstone J, Holeva M et al. (2014) Comparative and collaborative studies for the validation of a nested PCR for the detection of // | + | 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 // |
- | Cho MS, Kang MJ, Kim CK, Seol YJ, Hahn JH, Park SC, Hwang DJ, Ahn TY, Park DH, Lim CK et al. (2011) Sensitive and specific detection of // | + | Cho MS, Kang MJ, Kim CK, Seol YJ, Hahn JH, Park SC, Hwang DJ, Ahn TY, Park DH, Lim CK, Park DS (2011). Sensitive and specific detection of // |
- | 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 // | + | 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 // |
- | Cruz L, Sousa-Santos M (1999) Optimizing PCR technique for large scale diagnosis of angular leaf spot of strawberry in // | + | Cruz L, Sousa-Santos M (1999). Optimizing PCR technique for large scale diagnosis of angular leaf spot of strawberry in // |
- | Cubero J, Ayllón MA, Gell I, Melgarejo P, De Cal A, Martín-Sánchez PM, Pérez-Jiménez RM, Soria C, Segundo E, Larena I (2009) Detection of strawberry pathogens by real-time PCR. Acta Hortic. 842: 263-266. DOI: [[https:// | + | Cubero J, Ayllón MA, Gell I, Melgarejo P, De Cal A, Martín-Sánchez PM, Pérez-Jiménez RM, Soria C, Segundo E, Larena I (2009). Detection of strawberry pathogens by real-time PCR. Acta Hortic. 842: 263-266. DOI: [[https:// |
- | Cubero J, Graham JH (2002) Genetic relationship among worldwide strains of // | + | Cubero J, Graham JH (2002). Genetic relationship among worldwide strains of // |
- | Cubero J, Graham JH (2005) Quantitative real-time polymerase chain reaction for bacterial enumeration and allelic discrimination to differentiate // | + | Cubero J, Graham JH (2005). Quantitative real-time polymerase chain reaction for bacterial enumeration and allelic discrimination to differentiate // |
- | Cui Z, Ojaghian MR, Tao Z, Kakar KU, Zeng J, Zhao W, Duan Y, Vera Cruz CM, Li B, Zhu B, et al. (2016) Multiplex PCR assay for simultaneous detection of six major bacterial pathogens of rice. J. Appl. Microbiol.120, | + | 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, |
- | De Paiva BAR, Wendland A, Teixeira NC, Ferreira MASV (2020) Rapid detection of // | + | De Paiva BAR, Wendland A, Teixeira NC, Ferreira MASV (2020). Rapid detection of // |
- | Fernandes C, Albuquerque P, Sousa R, Cruz L, Tavares F (2017) Multiple DNA markers for identification of // | + | Fernandes C, Albuquerque P, Sousa R, Cruz L, Tavares F (2017). Multiple DNA markers for identification of // |
- | Fonseca, NP, Felestrino ÉB, Caneschi WL, Sanchez AB, CordeiroIF, Lemes CGC, Assis RAB, Carvalho FMS, Ferro JA, Varani AM et al. (2019) Detection and identification of // | + | 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 // |
- | Garita-Cambronero J, Palacio-Bielsa A, López MM, Cubero J (2017) Pan-genomic analysis permits differentiation of virulent and non-virulent strains of // | + | Garita-Cambronero J, Palacio-Bielsa A, López MM, Cubero J (2017). Pan-genomic analysis permits differentiation of virulent and non-virulent strains of // |
- | 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 // | + | 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 // |
- | Hartung J (1996) Rapid and sensitive colorimetric detection of // | + | Hartung J, Pruvost OP, Villemot I, Alvarez A (1996). Rapid and sensitive colorimetric detection of // |
- | Hartung JS, Pooler MR (1997) Immunocapture and multiplexed-PCR assay for // | + | Hartung JS, Pooler MR (1997). Immunocapture and multiplexed-PCR assay for // |
- | Immanuel T, Taylor R, Keeling S, Brosnahan C, Alexander B (2020) Discrimination between viable and dead // | + | Immanuel T, Taylor R, Keeling S, Brosnahan C, Alexander B (2020). Discrimination between viable and dead // |
- | 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 // | + | 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 // |
- | 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 (// | + | 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 (// |
- | 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 // | + | 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 // |
- | Kang MJ, Shim JK, Cho MS, Seol YJ, Hahn JH, Hwang DJ, Park DS (2008) Specific detection of // | + | Kang MJ, Shim JK, Cho MS, Seol YJ, Hahn JH, Hwang DJ, Park DS (2008). Specific detection of // |
- | Khoodoo MHR, Sahin F, Jaufeerally-Fakim Y (2005) Sensitive detection of // | + | Khoodoo MHR, Sahin F, Jaufeerally-Fakim Y (2005). Sensitive detection of // |
- | Koenraadt H, van Betteray B, Germain R, Hiddink G, Jones JB, Oosterhof J (2009) Development of specific primers for the molecular detection of bacterial spot of pepper and tomato. Acta Hortic. 808: 99-102. DOI: [[https:// | + | Koenraadt H, van Betteray B, Germain R, Hiddink G, Jones JB, Oosterhof J (2009). Development of specific primers for the molecular detection of bacterial spot of pepper and tomato. Acta Hortic. 808: 99-102. DOI: [[https:// |
- | Kositcharoenkul N, Chatchawankanphanich O, Bhunchoth A, Kositratana W (2011) Detection of // | + | Kositcharoenkul N, Chatchawankanphanich O, Bhunchoth A, Kositratana W (2011). Detection of // |
- | 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 // | + | 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 // |
- | 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 // | + | 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 // |
- | Langlois PA, Snelling J, Hamilton JP, Bragard C, Koebnik R, Verdier V, Triplett LR, Blom J, Tisserat NA, Leach JE (2017) Characterization of the // | + | Langlois PA, Snelling J, Hamilton JP, Bragard C, Koebnik R, Verdier V, Triplett LR, Blom J, Tisserat NA, Leach JE (2017). Characterization of the // |
- | Larrea-Sarmiento A, Dhakal U, Boluk G, Fatdal L, Alvarez A, Strayer-Scherer A, Paret M, Jones J, Jenkins D, Arif M (2018) Development of a genome-informed loop-mediated isothermal amplification assay for rapid and specific detection of // | + | Larrea-Sarmiento A, Dhakal U, Boluk G, Fatdal L, Alvarez A, Strayer-Scherer A, Paret M, Jones J, Jenkins D, Arif M (2018). Development of a genome-informed loop-mediated isothermal amplification assay for rapid and specific detection of // |
- | Li W, Lee SY, Back CG, Ten LN, Jung HY (2019) Loop-mediated isothermal amplification for the detection of // | + | Li W, Lee SY, Back CG, Ten LN, Jung HY (2019). Loop-mediated isothermal amplification for the detection of // |
- | Maes M, Garbeva P (1995) Development of a PCR-based detection method for // | + | Maes M, Garbeva P (1995). Development of a PCR-based detection method for // |
- | Martins L, Fernandes C, Albuquerque P, Tavares F (2019) Assessment of // | + | Martins L, Fernandes C, Albuquerque P, Tavares F (2019). Assessment of // |
- | Mavrodieva V, Levy L, Gabriel DW (2004) Improved sampling methods for real-time polymerase chain reaction diagnosis of citrus canker from field samples. Phytopathology 94: 61-68. DOI: [[https:// | + | Mavrodieva V, Levy L, Gabriel DW (2004). Improved sampling methods for real-time polymerase chain reaction diagnosis of citrus canker from field samples. Phytopathology 94: 61-68. DOI: [[https:// |
- | Moltmann E, Zimmermann C (2005) Detection of // | + | Moltmann E, Zimmermann C (2005). Detection of // |
- | Moretti C, Amatulli MT, Buonaurio R (2009) PCR-based assay for the detection of // | + | Moretti C, Amatulli MT, Buonaurio R (2009). PCR-based assay for the detection of // |
- | Palacio-Bielsa A, Cubero J, Cambra MA, Collados R, Berruete IM, López MM (2011) Development of an efficient real-time quantitative PCR protocol for detection of // | + | Palacio-Bielsa A, Cubero J, Cambra MA, Collados R, Berruete IM, López MM (2011). Development of an efficient real-time quantitative PCR protocol for detection of // |
- | Park SY, Lee YS, Koh YJ, Hur JS, Jung JS (2010) Detection of // | + | Park SY, Lee YS, Koh YJ, Hur JS, Jung JS (2010). Detection of // |
- | Pečenka J, Kocanová M, Baránek M, Gazdík F, Ragasová L, Peňázová E, Ĉechová J, Beran P, Eichmeier A (2020) Species-specific PCR primers for the detection of poorly distinguishable // | + | Pečenka J, Kocanová M, Baránek M, Gazdík F, Ragasová L, Peňázová E, Ĉechová J, Beran P, Eichmeier A (2020). Species-specific PCR primers for the detection of poorly distinguishable // |
- | Rigano LA, Marano MR, Castagnaro AP, Do Amaral AM, Vojnov AA (2010) Rapid and sensitive detection of Citrus Bacterial Canker by loop-mediated isothermal amplification combined with simple visual evaluation methods. BMC Microbiol. 10: 176. DOI: [[https:// | + | Rigano LA, Marano MR, Castagnaro AP, Do Amaral AM, Vojnov AA (2010). Rapid and sensitive detection of Citrus Bacterial Canker by loop-mediated isothermal amplification combined with simple visual evaluation methods. BMC Microbiol. 10: 176. DOI: [[https:// |
- | Robène I, Perret M, Jouen E, Escalon A, Maillot MV, Chabirand A, Moreau A, Laurent A, Chiroleu F, Pruvost O (2015) Development and validation of a real-time quantitative PCR assay to detect // | + | Robène I, Perret M, Jouen E, Escalon A, Maillot MV, Chabirand A, Moreau A, Laurent A, Chiroleu F, Pruvost O (2015). Development and validation of a real-time quantitative PCR assay to detect // |
- | Robène I, Maillot-Lebon V, Chabirand A, Moreau A, Becker N, Moumène A, Rieux A, Campos P, Gagnevin L, Gaudeul M, et al. (2020) Development and comparative validation of genomic-driven PCR-based assays to detect // | + | Robène I, Maillot-Lebon V, Chabirand A, Moreau A, Becker N, Moumène A, Rieux A, Campos P, Gagnevin L, Gaudeul M, Baider C, Chiroleu F, Pruvost O (2020). Development and comparative validation of genomic-driven PCR-based assays to detect // |
- | Robène-Soustrade I, Laurent P, Gagnevin L, Jouen E, Pruvost O (2006) Specific detection of // | + | Robène-Soustrade I, Laurent P, Gagnevin L, Jouen E, Pruvost O (2006). Specific detection of // |
- | Robène-Soustrade I, Legrand D, Gagnevin L, Chiroleu F, Laurent A, Pruvost O (2020) Multiplex nested PCR for detection of // | + | Robène-Soustrade I, Legrand D, Gagnevin L, Chiroleu F, Laurent A, Pruvost O (2020). Multiplex nested PCR for detection of // |
- | Sakthivel N, Mortensen CN, Mathur SB (2001) Detection of // | + | Sakthivel N, Mortensen CN, Mathur SB (2001). Detection of // |
- | Shen YP, Zou LF, Li YR, Zou HS, Liu XL, Chen GY (2012) Xoryp_08180 of // | + | Shen YP, Zou LF, Li YR, Zou HS, Liu XL, Chen GY (2012). Xoryp_08180 of // |
- | Singhal N, Kumar M, Kanaujia PK, Virdi JS (2015) MALDI-TOF mass spectrometry: | + | Singhal N, Kumar M, Kanaujia PK, Virdi JS (2015). MALDI-TOF mass spectrometry: |
- | Stehlíková D, Beran P, Cohen SP, Curn V (2020) Development of real-time and colorimetric loop mediated isothermal amplification assay for detection of // | + | Stehlíková D, Beran P, Cohen SP, Curn V (2020). Development of real-time and colorimetric loop mediated isothermal amplification assay for detection of // |
- | Stöger A, Ruppitsch W (2004) A rapid and sensitive method for the detection of Xanthomonas fragariae, causal agent of angular leafspot disease in strawberry plants. J. Microbiol. Methods 58: 281-284. DOI: [[https:// | + | Stöger A, Ruppitsch W (2004). A rapid and sensitive method for the detection of Xanthomonas fragariae, causal agent of angular leafspot disease in strawberry plants. J. Microbiol. Methods 58: 281-284. DOI: [[https:// |
- | Strayer AL, Jeyaprakash A, Minsavage GV, Timilsina S, Vallad GE, Jones JB, Paret ML (2016) A multiplex real-time PCR assay differentiates four // | + | Strayer AL, Jeyaprakash A, Minsavage GV, Timilsina S, Vallad GE, Jones JB, Paret ML (2016). A multiplex real-time PCR assay differentiates four // |
- | Strayer-Scherer A, Jones JB, Paret ML (2019) Recombinase polymerase amplification assay for field detection of tomato bacterial spot pathogens. Phytopathology 109: 690-700. DOI: [[https:// | + | Strayer-Scherer A, Jones JB, Paret ML (2019). Recombinase polymerase amplification assay for field detection of tomato bacterial spot pathogens. Phytopathology 109: 690-700. DOI: [[https:// |
- | Suk Park D, Wook Hyun J, Jin Park Y, Sun Kim J, Wan Kang H, Ho Hahn J, Joo Go S (2006) Sensitive and specific detection of // | + | Suk Park D, Wook Hyun J, Jin Park Y, Sun Kim J, Wan Kang H, Ho Hahn J, Joo Go S (2006). Sensitive and specific detection of // |
- | Turechek WW, Hartung JS, McCallister J (2008) Development and optimization of a real-time detection assay for // | + | Turechek WW, Hartung JS, McCallister J (2008). Development and optimization of a real-time detection assay for // |
- | Vandroemme J, Baeyen S, Van Vaerenbergh J, De Vos, Maes M (2008) Sensitive real-time PCR detection of // | + | Vandroemme J, Baeyen S, Van Vaerenbergh J, De Vos, Maes M (2008). Sensitive real-time PCR detection of // |
- | Wang H, Turechek WW (2016) A loop-mediated isothermal amplification assay and sample preparation procedure for sensitive detection of // | + | Wang H, Turechek WW (2016). A loop-mediated isothermal amplification assay and sample preparation procedure for sensitive detection of // |
- | Wang H, Turechek WW (2020) Detection of viable // | + | Wang H, Turechek WW (2020). Detection of viable // |
- | Webber JB, Putnam M, Serdani M, Pscheidt JW, Wiman NG, Stockwell VO (2020) Characterization of isolates of // | + | Webber JB, Putnam M, Serdani M, Pscheidt JW, Wiman NG, Stockwell VO (2020). Characterization of isolates of // |
+ | |||
+ | Webster J, Kehoe MA, Nogarotto E, Falconer L, Donovan NJ, Chapman TA (2022). Using genomics to design a pathovar-specific loop-mediated isothermal amplification (LAMP) assay, for the improved detection of // | ||
+ | |||
+ | Zhu Z, Li R, Zhang H, Wang J, Lu Y, Zhang D, Yang L (2022). PAM-free loop-mediated isothermal amplification coupled with CRISPR/ | ||
===== Further reading ===== | ===== Further reading ===== |