Distinctively variable sequence-based nuclear DNA markers for multilocus phylogeography of the soybean- and rice-infecting fungal pathogen Rhizoctonia solani AG-1 IA
Autor(a) principal: | |
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Data de Publicação: | 2009 |
Outros Autores: | , , |
Tipo de documento: | Artigo |
Idioma: | eng |
Título da fonte: | Repositório Institucional da UNESP |
Texto Completo: | http://dx.doi.org/10.1590/S1415-47572009005000063 http://hdl.handle.net/11449/4176 |
Resumo: | A series of multilocus sequence-based nuclear DNA markers was developed to infer the phylogeographical history of the Basidiomycetous fungal pathogen Rhizoctonia solani AG-1 IA infecting rice and soybean worldwide. The strategy was based on sequencing of cloned genomic DNA fragments (previously used as RFLP probes) and subsequent screening of fungal isolates to detect single nucleotide polymorphisms (SNPs). Ten primer pairs were designed based on these sequences, which resulted in PCR amplification of 200-320 bp size products and polymorphic sequences in all markers analyzed. By direct sequencing we identified both homokaryon and heterokaryon (i.e. dikaryon) isolates at each marker. Cloning the PCR products effectively estimated the allelic phase from heterokaryotic isolates. Information content varied among markers from 0.5 to 5.9 mutations per 100 bp. Thus, the former RFLP codominant probes were successfully converted into six distinctively variable sequence-based nuclear DNA markers. Rather than discarding low polymorphism loci, the combination of these distinctively variable anonymous nuclear markers would constitute an asset for the unbiased estimate of the phylogeographical parameters such as population sizes and divergent times, providing a more reliable species history that shaped the current population structure of R. solani AG-1 IA. |
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Distinctively variable sequence-based nuclear DNA markers for multilocus phylogeography of the soybean- and rice-infecting fungal pathogen Rhizoctonia solani AG-1 IAmultilocus genotypingPolymorphismallelic discriminationprimer designA series of multilocus sequence-based nuclear DNA markers was developed to infer the phylogeographical history of the Basidiomycetous fungal pathogen Rhizoctonia solani AG-1 IA infecting rice and soybean worldwide. The strategy was based on sequencing of cloned genomic DNA fragments (previously used as RFLP probes) and subsequent screening of fungal isolates to detect single nucleotide polymorphisms (SNPs). Ten primer pairs were designed based on these sequences, which resulted in PCR amplification of 200-320 bp size products and polymorphic sequences in all markers analyzed. By direct sequencing we identified both homokaryon and heterokaryon (i.e. dikaryon) isolates at each marker. Cloning the PCR products effectively estimated the allelic phase from heterokaryotic isolates. Information content varied among markers from 0.5 to 5.9 mutations per 100 bp. Thus, the former RFLP codominant probes were successfully converted into six distinctively variable sequence-based nuclear DNA markers. Rather than discarding low polymorphism loci, the combination of these distinctively variable anonymous nuclear markers would constitute an asset for the unbiased estimate of the phylogeographical parameters such as population sizes and divergent times, providing a more reliable species history that shaped the current population structure of R. solani AG-1 IA.Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)Universidade Estadual Paulista Faculdade de Ciências Agrárias e Veterinárias Departamento de TecnologiaUniversity of Minnesota Department of Plant PathologyUniversidade Estadual Paulista Engenharia Rural e Solos Departamento de FitossanidadeSwiss Federal of Technology Zurich Institute of Integrative Biology Plant PathologyUniversidade Estadual Paulista Faculdade de Ciências Agrárias e Veterinárias Departamento de TecnologiaUniversidade Estadual Paulista Engenharia Rural e Solos Departamento de FitossanidadeFAPESP: 02/13881-0ETH: TH-16/06-1Sociedade Brasileira de GenéticaUniversidade Estadual Paulista (Unesp)University of Minnesota Department of Plant PathologySwiss Federal of Technology Zurich Institute of Integrative Biology Plant PathologyCiampi, Maisa B. [UNESP]Gale, Liane RosewichLemos, Eliana G. de Macedo [UNESP]Ceresini, Paulo C. [UNESP]2014-05-20T13:17:53Z2014-05-20T13:17:53Z2009-01-01info:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/article840-846application/pdfhttp://dx.doi.org/10.1590/S1415-47572009005000063Genetics and Molecular Biology. Sociedade Brasileira de Genética, v. 32, n. 4, p. 840-846, 2009.1415-4757http://hdl.handle.net/11449/417610.1590/S1415-47572009005000063S1415-47572009000400027WOS:000272182700027S1415-47572009000400027.pdfSciELOreponame:Repositório Institucional da UNESPinstname:Universidade Estadual Paulista (UNESP)instacron:UNESPengGenetics and Molecular Biology1.4930,638info:eu-repo/semantics/openAccess2024-06-07T15:32:22Zoai:repositorio.unesp.br:11449/4176Repositório InstitucionalPUBhttp://repositorio.unesp.br/oai/requestopendoar:29462024-08-05T21:16:26.442729Repositório Institucional da UNESP - Universidade Estadual Paulista (UNESP)false |
dc.title.none.fl_str_mv |
Distinctively variable sequence-based nuclear DNA markers for multilocus phylogeography of the soybean- and rice-infecting fungal pathogen Rhizoctonia solani AG-1 IA |
title |
Distinctively variable sequence-based nuclear DNA markers for multilocus phylogeography of the soybean- and rice-infecting fungal pathogen Rhizoctonia solani AG-1 IA |
spellingShingle |
Distinctively variable sequence-based nuclear DNA markers for multilocus phylogeography of the soybean- and rice-infecting fungal pathogen Rhizoctonia solani AG-1 IA Ciampi, Maisa B. [UNESP] multilocus genotyping Polymorphism allelic discrimination primer design |
title_short |
Distinctively variable sequence-based nuclear DNA markers for multilocus phylogeography of the soybean- and rice-infecting fungal pathogen Rhizoctonia solani AG-1 IA |
title_full |
Distinctively variable sequence-based nuclear DNA markers for multilocus phylogeography of the soybean- and rice-infecting fungal pathogen Rhizoctonia solani AG-1 IA |
title_fullStr |
Distinctively variable sequence-based nuclear DNA markers for multilocus phylogeography of the soybean- and rice-infecting fungal pathogen Rhizoctonia solani AG-1 IA |
title_full_unstemmed |
Distinctively variable sequence-based nuclear DNA markers for multilocus phylogeography of the soybean- and rice-infecting fungal pathogen Rhizoctonia solani AG-1 IA |
title_sort |
Distinctively variable sequence-based nuclear DNA markers for multilocus phylogeography of the soybean- and rice-infecting fungal pathogen Rhizoctonia solani AG-1 IA |
author |
Ciampi, Maisa B. [UNESP] |
author_facet |
Ciampi, Maisa B. [UNESP] Gale, Liane Rosewich Lemos, Eliana G. de Macedo [UNESP] Ceresini, Paulo C. [UNESP] |
author_role |
author |
author2 |
Gale, Liane Rosewich Lemos, Eliana G. de Macedo [UNESP] Ceresini, Paulo C. [UNESP] |
author2_role |
author author author |
dc.contributor.none.fl_str_mv |
Universidade Estadual Paulista (Unesp) University of Minnesota Department of Plant Pathology Swiss Federal of Technology Zurich Institute of Integrative Biology Plant Pathology |
dc.contributor.author.fl_str_mv |
Ciampi, Maisa B. [UNESP] Gale, Liane Rosewich Lemos, Eliana G. de Macedo [UNESP] Ceresini, Paulo C. [UNESP] |
dc.subject.por.fl_str_mv |
multilocus genotyping Polymorphism allelic discrimination primer design |
topic |
multilocus genotyping Polymorphism allelic discrimination primer design |
description |
A series of multilocus sequence-based nuclear DNA markers was developed to infer the phylogeographical history of the Basidiomycetous fungal pathogen Rhizoctonia solani AG-1 IA infecting rice and soybean worldwide. The strategy was based on sequencing of cloned genomic DNA fragments (previously used as RFLP probes) and subsequent screening of fungal isolates to detect single nucleotide polymorphisms (SNPs). Ten primer pairs were designed based on these sequences, which resulted in PCR amplification of 200-320 bp size products and polymorphic sequences in all markers analyzed. By direct sequencing we identified both homokaryon and heterokaryon (i.e. dikaryon) isolates at each marker. Cloning the PCR products effectively estimated the allelic phase from heterokaryotic isolates. Information content varied among markers from 0.5 to 5.9 mutations per 100 bp. Thus, the former RFLP codominant probes were successfully converted into six distinctively variable sequence-based nuclear DNA markers. Rather than discarding low polymorphism loci, the combination of these distinctively variable anonymous nuclear markers would constitute an asset for the unbiased estimate of the phylogeographical parameters such as population sizes and divergent times, providing a more reliable species history that shaped the current population structure of R. solani AG-1 IA. |
publishDate |
2009 |
dc.date.none.fl_str_mv |
2009-01-01 2014-05-20T13:17:53Z 2014-05-20T13:17:53Z |
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/10.1590/S1415-47572009005000063 Genetics and Molecular Biology. Sociedade Brasileira de Genética, v. 32, n. 4, p. 840-846, 2009. 1415-4757 http://hdl.handle.net/11449/4176 10.1590/S1415-47572009005000063 S1415-47572009000400027 WOS:000272182700027 S1415-47572009000400027.pdf |
url |
http://dx.doi.org/10.1590/S1415-47572009005000063 http://hdl.handle.net/11449/4176 |
identifier_str_mv |
Genetics and Molecular Biology. Sociedade Brasileira de Genética, v. 32, n. 4, p. 840-846, 2009. 1415-4757 10.1590/S1415-47572009005000063 S1415-47572009000400027 WOS:000272182700027 S1415-47572009000400027.pdf |
dc.language.iso.fl_str_mv |
eng |
language |
eng |
dc.relation.none.fl_str_mv |
Genetics and Molecular Biology 1.493 0,638 |
dc.rights.driver.fl_str_mv |
info:eu-repo/semantics/openAccess |
eu_rights_str_mv |
openAccess |
dc.format.none.fl_str_mv |
840-846 application/pdf |
dc.publisher.none.fl_str_mv |
Sociedade Brasileira de Genética |
publisher.none.fl_str_mv |
Sociedade Brasileira de Genética |
dc.source.none.fl_str_mv |
SciELO reponame:Repositório Institucional da UNESP instname:Universidade Estadual Paulista (UNESP) instacron:UNESP |
instname_str |
Universidade Estadual Paulista (UNESP) |
instacron_str |
UNESP |
institution |
UNESP |
reponame_str |
Repositório Institucional da UNESP |
collection |
Repositório Institucional da UNESP |
repository.name.fl_str_mv |
Repositório Institucional da UNESP - Universidade Estadual Paulista (UNESP) |
repository.mail.fl_str_mv |
|
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1808129303293984768 |