Detection and identification of Xanthomonas pathotypes associated with citrus diseases using comparative genomics and multiplex PCR

Detalhes bibliográficos
Autor(a) principal: Fonseca, Natasha P.
Data de Publicação: 2019
Outros Autores: 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.
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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spelling 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
dc.relation.none.fl_str_mv PeerJ
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instname_str Universidade Estadual Paulista (UNESP)
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reponame_str Repositório Institucional da UNESP
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repository.name.fl_str_mv Repositório Institucional da UNESP - Universidade Estadual Paulista (UNESP)
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