Detection and identification of Xanthomonas pathotypes associated with citrus diseases using comparative genomics and multiplex PCR
Autor(a) principal: | |
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Data de Publicação: | 2019 |
Outros Autores: | , , , , , , , , , , , , , , |
Tipo de documento: | Artigo |
Idioma: | eng |
Título da fonte: | Repositório Institucional da UNESP |
Texto Completo: | http://dx.doi.org/10.7717/peerj.7676 http://hdl.handle.net/11449/199563 |
Resumo: | Background. In Citrus cultures, three species of Xanthomonas are known to cause distinct diseases. X. citri subsp. citri patothype A, X. fuscans subsp. aurantifolii pathotypes B and C, and X. alfalfae subsp. citrumelonis, are the causative agents of cancrosis A, B, C, and citrus bacterial spots, respectively. Although these species exhibit different levels of virulence and aggressiveness, only limited alternatives are currently available for proper and early detection of these diseases in the fields. The present study aimed to develop a new molecular diagnostic method based on genomic sequences derived from the four species of Xanthomonas. Results. Using comparative genomics approaches, primers were synthesized for the identification of the four causative agents of citrus diseases. These primers were validated for their specificity to their target DNA by both conventional and multiplex PCR. Upon evaluation, their sensitivity was found to be 0.02 ng/µl in vitro and 1.5 × 104 CFU ml−1 in infected leaves. Additionally, none of the primers were able to generate amplicons in 19 other genomes of Xanthomonas not associated with Citrus and one species of Xylella, the causal agent of citrus variegated chlorosis (CVC). This denotes strong specificity of the primers for the different species of Xanthomonas investigated in this study. Conclusions. We demonstrated that these markers can be used as potential candidates for performing in vivo molecular diagnosis exclusively for citrus-associated Xanthomonas. The bioinformatics pipeline developed in this study to design specific genomic regions is capable of generating specific primers. It is freely available and can be utilized for any other model organism. |
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Detection and identification of Xanthomonas pathotypes associated with citrus diseases using comparative genomics and multiplex PCRCitrus cankerComparative genomics analysisMolecular diagnosticMultiplex PCRXanthomonasBackground. In Citrus cultures, three species of Xanthomonas are known to cause distinct diseases. X. citri subsp. citri patothype A, X. fuscans subsp. aurantifolii pathotypes B and C, and X. alfalfae subsp. citrumelonis, are the causative agents of cancrosis A, B, C, and citrus bacterial spots, respectively. Although these species exhibit different levels of virulence and aggressiveness, only limited alternatives are currently available for proper and early detection of these diseases in the fields. The present study aimed to develop a new molecular diagnostic method based on genomic sequences derived from the four species of Xanthomonas. Results. Using comparative genomics approaches, primers were synthesized for the identification of the four causative agents of citrus diseases. These primers were validated for their specificity to their target DNA by both conventional and multiplex PCR. Upon evaluation, their sensitivity was found to be 0.02 ng/µl in vitro and 1.5 × 104 CFU ml−1 in infected leaves. Additionally, none of the primers were able to generate amplicons in 19 other genomes of Xanthomonas not associated with Citrus and one species of Xylella, the causal agent of citrus variegated chlorosis (CVC). This denotes strong specificity of the primers for the different species of Xanthomonas investigated in this study. Conclusions. We demonstrated that these markers can be used as potential candidates for performing in vivo molecular diagnosis exclusively for citrus-associated Xanthomonas. The bioinformatics pipeline developed in this study to design specific genomic regions is capable of generating specific primers. It is freely available and can be utilized for any other model organism.Fundo de Defesa da CitriculturaCoordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)Fundação de Amparo à Pesquisa do Estado de Minas Gerais (FAPEMIG)Núcleo de Pesquisas em Ciências Biológicas Universidade Federal de Ouro PretoDepartamento de Tecnologia Faculdade de Ciências Agrárias e Veterinárias de Jaboticabal Universidade Estadual Paulista-UnespDepartamento de Fitopatologia e Nematologia Escola Superior de Agricultura ‘‘Luiz de Queiroz’’Departamento de Bioquímica Instituto de Química Universidade de São PauloInstituto de Computação Universidade Estadual de CampinasFaculdade de Computação Universidade Federal de Mato Grosso do SulDepartamento de Ciências Biológicas Universidade Federal de Ouro PretoDepartamento de Tecnologia Faculdade de Ciências Agrárias e Veterinárias de Jaboticabal Universidade Estadual Paulista-UnespFundo de Defesa da Citricultura: 007/2015 SIAFEM 025139CAPES: 3385/2013CNPq: 481226/2013-3FAPEMIG: APQ-02387-14CAPES: CFP 51/2013Universidade Federal de Ouro PretoUniversidade Estadual Paulista (Unesp)Escola Superior de Agricultura ‘‘Luiz de Queiroz’’Universidade de São Paulo (USP)Universidade Estadual de Campinas (UNICAMP)Universidade Federal de Mato Grosso do Sul (UFMS)Fonseca, Natasha P.Felestrino, Érica B.Caneschi, Washington L.Sanchez, Angélica B.Cordeiro, Isabella F.Lemes, Camila G.C.Assis, Renata A.B.Carvalho, Flávia M.S. [UNESP]Ferro, Jesus A. [UNESP]Varani, Alessandro M. [UNESP]Belasque, JoséSetubal, Joao C.Telles, Guilherme P.Aguena, Deiviston S.Almeida, Nalvo F.Moreira, Leandro M.2020-12-12T01:43:17Z2020-12-12T01:43:17Z2019-01-01info:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articlehttp://dx.doi.org/10.7717/peerj.7676PeerJ, v. 2019, n. 10, 2019.2167-8359http://hdl.handle.net/11449/19956310.7717/peerj.76762-s2.0-85074140663Scopusreponame:Repositório Institucional da UNESPinstname:Universidade Estadual Paulista (UNESP)instacron:UNESPengPeerJinfo:eu-repo/semantics/openAccess2024-06-07T15:32:12Zoai:repositorio.unesp.br:11449/199563Repositório InstitucionalPUBhttp://repositorio.unesp.br/oai/requestopendoar:29462024-08-05T20:34:09.114535Repositório Institucional da UNESP - Universidade Estadual Paulista (UNESP)false |
dc.title.none.fl_str_mv |
Detection and identification of Xanthomonas pathotypes associated with citrus diseases using comparative genomics and multiplex PCR |
title |
Detection and identification of Xanthomonas pathotypes associated with citrus diseases using comparative genomics and multiplex PCR |
spellingShingle |
Detection and identification of Xanthomonas pathotypes associated with citrus diseases using comparative genomics and multiplex PCR Fonseca, Natasha P. Citrus canker Comparative genomics analysis Molecular diagnostic Multiplex PCR Xanthomonas |
title_short |
Detection and identification of Xanthomonas pathotypes associated with citrus diseases using comparative genomics and multiplex PCR |
title_full |
Detection and identification of Xanthomonas pathotypes associated with citrus diseases using comparative genomics and multiplex PCR |
title_fullStr |
Detection and identification of Xanthomonas pathotypes associated with citrus diseases using comparative genomics and multiplex PCR |
title_full_unstemmed |
Detection and identification of Xanthomonas pathotypes associated with citrus diseases using comparative genomics and multiplex PCR |
title_sort |
Detection and identification of Xanthomonas pathotypes associated with citrus diseases using comparative genomics and multiplex PCR |
author |
Fonseca, Natasha P. |
author_facet |
Fonseca, Natasha P. Felestrino, Érica B. Caneschi, Washington L. Sanchez, Angélica B. Cordeiro, Isabella F. Lemes, Camila G.C. Assis, Renata A.B. Carvalho, Flávia M.S. [UNESP] Ferro, Jesus A. [UNESP] Varani, Alessandro M. [UNESP] Belasque, José Setubal, Joao C. Telles, Guilherme P. Aguena, Deiviston S. Almeida, Nalvo F. Moreira, Leandro M. |
author_role |
author |
author2 |
Felestrino, Érica B. Caneschi, Washington L. Sanchez, Angélica B. Cordeiro, Isabella F. Lemes, Camila G.C. Assis, Renata A.B. Carvalho, Flávia M.S. [UNESP] Ferro, Jesus A. [UNESP] Varani, Alessandro M. [UNESP] Belasque, José Setubal, Joao C. Telles, Guilherme P. Aguena, Deiviston S. Almeida, Nalvo F. Moreira, Leandro M. |
author2_role |
author author author author author author author author author author author author author author author |
dc.contributor.none.fl_str_mv |
Universidade Federal de Ouro Preto Universidade Estadual Paulista (Unesp) Escola Superior de Agricultura ‘‘Luiz de Queiroz’’ Universidade de São Paulo (USP) Universidade Estadual de Campinas (UNICAMP) Universidade Federal de Mato Grosso do Sul (UFMS) |
dc.contributor.author.fl_str_mv |
Fonseca, Natasha P. Felestrino, Érica B. Caneschi, Washington L. Sanchez, Angélica B. Cordeiro, Isabella F. Lemes, Camila G.C. Assis, Renata A.B. Carvalho, Flávia M.S. [UNESP] Ferro, Jesus A. [UNESP] Varani, Alessandro M. [UNESP] Belasque, José Setubal, Joao C. Telles, Guilherme P. Aguena, Deiviston S. Almeida, Nalvo F. Moreira, Leandro M. |
dc.subject.por.fl_str_mv |
Citrus canker Comparative genomics analysis Molecular diagnostic Multiplex PCR Xanthomonas |
topic |
Citrus canker Comparative genomics analysis Molecular diagnostic Multiplex PCR Xanthomonas |
description |
Background. In Citrus cultures, three species of Xanthomonas are known to cause distinct diseases. X. citri subsp. citri patothype A, X. fuscans subsp. aurantifolii pathotypes B and C, and X. alfalfae subsp. citrumelonis, are the causative agents of cancrosis A, B, C, and citrus bacterial spots, respectively. Although these species exhibit different levels of virulence and aggressiveness, only limited alternatives are currently available for proper and early detection of these diseases in the fields. The present study aimed to develop a new molecular diagnostic method based on genomic sequences derived from the four species of Xanthomonas. Results. Using comparative genomics approaches, primers were synthesized for the identification of the four causative agents of citrus diseases. These primers were validated for their specificity to their target DNA by both conventional and multiplex PCR. Upon evaluation, their sensitivity was found to be 0.02 ng/µl in vitro and 1.5 × 104 CFU ml−1 in infected leaves. Additionally, none of the primers were able to generate amplicons in 19 other genomes of Xanthomonas not associated with Citrus and one species of Xylella, the causal agent of citrus variegated chlorosis (CVC). This denotes strong specificity of the primers for the different species of Xanthomonas investigated in this study. Conclusions. We demonstrated that these markers can be used as potential candidates for performing in vivo molecular diagnosis exclusively for citrus-associated Xanthomonas. The bioinformatics pipeline developed in this study to design specific genomic regions is capable of generating specific primers. It is freely available and can be utilized for any other model organism. |
publishDate |
2019 |
dc.date.none.fl_str_mv |
2019-01-01 2020-12-12T01:43:17Z 2020-12-12T01:43:17Z |
dc.type.status.fl_str_mv |
info:eu-repo/semantics/publishedVersion |
dc.type.driver.fl_str_mv |
info:eu-repo/semantics/article |
format |
article |
status_str |
publishedVersion |
dc.identifier.uri.fl_str_mv |
http://dx.doi.org/10.7717/peerj.7676 PeerJ, v. 2019, n. 10, 2019. 2167-8359 http://hdl.handle.net/11449/199563 10.7717/peerj.7676 2-s2.0-85074140663 |
url |
http://dx.doi.org/10.7717/peerj.7676 http://hdl.handle.net/11449/199563 |
identifier_str_mv |
PeerJ, v. 2019, n. 10, 2019. 2167-8359 10.7717/peerj.7676 2-s2.0-85074140663 |
dc.language.iso.fl_str_mv |
eng |
language |
eng |
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PeerJ |
dc.rights.driver.fl_str_mv |
info:eu-repo/semantics/openAccess |
eu_rights_str_mv |
openAccess |
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Scopus reponame:Repositório Institucional da UNESP instname:Universidade Estadual Paulista (UNESP) instacron:UNESP |
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Universidade Estadual Paulista (UNESP) |
instacron_str |
UNESP |
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UNESP |
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Repositório Institucional da UNESP |
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Repositório Institucional da UNESP |
repository.name.fl_str_mv |
Repositório Institucional da UNESP - Universidade Estadual Paulista (UNESP) |
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1808129221123375104 |