(GTG)5 MSP-PCR fingerprinting as a technique for discrimination of wine associated yeasts?
Autor(a) principal: | |
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Data de Publicação: | 2014 |
Outros Autores: | , , |
Tipo de documento: | Artigo |
Idioma: | eng |
Título da fonte: | Repositório Institucional da UFRGS |
Texto Completo: | http://hdl.handle.net/10183/225373 |
Resumo: | In microbiology, identification of all isolates by sequencing is still unfeasible in small research laboratories. Therefore, many yeast diversity studies follow a screening procedure consisting of clustering the yeast isolates using MSP-PCR fingerprinting, followed by identification of one or a few selected representatives of each cluster by sequencing. Although this procedure has been widely applied in the literature, it has not been properly validated. We evaluated a standardized protocol using MSP-PCR fingerprinting with the primers (GTG)5 and M13 for the discrimination of wine associated yeasts in South Brazil. Two datasets were used: yeasts isolated from bottled wines and vineyard environments. We compared the discriminatory power of both primers in a subset of 16 strains, choosing the primer (GTG)5 for further evaluation. Afterwards, we applied this technique to 245 strains, and compared the results with the identification obtained by partial sequencing of the LSU rRNA gene, considered as the gold standard. An array matrix was constructed for each dataset and used as input for clustering with two methods (hierarchical dendrograms and QAPGrid layout). For both yeast datasets, unrelated species were clustered in the same group. The sensitivity score of (GTG)5 MSP-PCR fingerprinting was high, but specificity was low. As a conclusion, the yeast diversity inferred in several previous studies may have been underestimated and some isolates were probably misidentified due to the compliance to this screening procedure. |
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Ramírez Castrillón, MauricioMendes, Sandra Denise CamargoInostroza-Ponta, MarioSilva, Patrícia Valente da2021-08-10T04:31:22Z20141932-6203http://hdl.handle.net/10183/225373000938899In microbiology, identification of all isolates by sequencing is still unfeasible in small research laboratories. Therefore, many yeast diversity studies follow a screening procedure consisting of clustering the yeast isolates using MSP-PCR fingerprinting, followed by identification of one or a few selected representatives of each cluster by sequencing. Although this procedure has been widely applied in the literature, it has not been properly validated. We evaluated a standardized protocol using MSP-PCR fingerprinting with the primers (GTG)5 and M13 for the discrimination of wine associated yeasts in South Brazil. Two datasets were used: yeasts isolated from bottled wines and vineyard environments. We compared the discriminatory power of both primers in a subset of 16 strains, choosing the primer (GTG)5 for further evaluation. Afterwards, we applied this technique to 245 strains, and compared the results with the identification obtained by partial sequencing of the LSU rRNA gene, considered as the gold standard. An array matrix was constructed for each dataset and used as input for clustering with two methods (hierarchical dendrograms and QAPGrid layout). For both yeast datasets, unrelated species were clustered in the same group. The sensitivity score of (GTG)5 MSP-PCR fingerprinting was high, but specificity was low. As a conclusion, the yeast diversity inferred in several previous studies may have been underestimated and some isolates were probably misidentified due to the compliance to this screening procedure.application/pdfengPLoS ONE. San Francisco. Vol. 9, no. 8 (Aug. 2014), e105870 [8] f.LevedurasVinhoImpressões digitais de DNA(GTG)5 MSP-PCR fingerprinting as a technique for discrimination of wine associated yeasts?Estrangeiroinfo:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/openAccessreponame:Repositório Institucional da UFRGSinstname:Universidade Federal do Rio Grande do Sul (UFRGS)instacron:UFRGSTEXT000938899.pdf.txt000938899.pdf.txtExtracted Texttext/plain46268http://www.lume.ufrgs.br/bitstream/10183/225373/2/000938899.pdf.txt83b21a4c65f155c1b7e8386c3851c4daMD52ORIGINAL000938899.pdfTexto completo (inglês)application/pdf524404http://www.lume.ufrgs.br/bitstream/10183/225373/1/000938899.pdf83485dcd11f02f8a8efa2ae6dd8880bfMD5110183/2253732023-01-18 06:02:08.189203oai:www.lume.ufrgs.br:10183/225373Repositório de PublicaçõesPUBhttps://lume.ufrgs.br/oai/requestopendoar:2023-01-18T08:02:08Repositório Institucional da UFRGS - Universidade Federal do Rio Grande do Sul (UFRGS)false |
dc.title.pt_BR.fl_str_mv |
(GTG)5 MSP-PCR fingerprinting as a technique for discrimination of wine associated yeasts? |
title |
(GTG)5 MSP-PCR fingerprinting as a technique for discrimination of wine associated yeasts? |
spellingShingle |
(GTG)5 MSP-PCR fingerprinting as a technique for discrimination of wine associated yeasts? Ramírez Castrillón, Mauricio Leveduras Vinho Impressões digitais de DNA |
title_short |
(GTG)5 MSP-PCR fingerprinting as a technique for discrimination of wine associated yeasts? |
title_full |
(GTG)5 MSP-PCR fingerprinting as a technique for discrimination of wine associated yeasts? |
title_fullStr |
(GTG)5 MSP-PCR fingerprinting as a technique for discrimination of wine associated yeasts? |
title_full_unstemmed |
(GTG)5 MSP-PCR fingerprinting as a technique for discrimination of wine associated yeasts? |
title_sort |
(GTG)5 MSP-PCR fingerprinting as a technique for discrimination of wine associated yeasts? |
author |
Ramírez Castrillón, Mauricio |
author_facet |
Ramírez Castrillón, Mauricio Mendes, Sandra Denise Camargo Inostroza-Ponta, Mario Silva, Patrícia Valente da |
author_role |
author |
author2 |
Mendes, Sandra Denise Camargo Inostroza-Ponta, Mario Silva, Patrícia Valente da |
author2_role |
author author author |
dc.contributor.author.fl_str_mv |
Ramírez Castrillón, Mauricio Mendes, Sandra Denise Camargo Inostroza-Ponta, Mario Silva, Patrícia Valente da |
dc.subject.por.fl_str_mv |
Leveduras Vinho Impressões digitais de DNA |
topic |
Leveduras Vinho Impressões digitais de DNA |
description |
In microbiology, identification of all isolates by sequencing is still unfeasible in small research laboratories. Therefore, many yeast diversity studies follow a screening procedure consisting of clustering the yeast isolates using MSP-PCR fingerprinting, followed by identification of one or a few selected representatives of each cluster by sequencing. Although this procedure has been widely applied in the literature, it has not been properly validated. We evaluated a standardized protocol using MSP-PCR fingerprinting with the primers (GTG)5 and M13 for the discrimination of wine associated yeasts in South Brazil. Two datasets were used: yeasts isolated from bottled wines and vineyard environments. We compared the discriminatory power of both primers in a subset of 16 strains, choosing the primer (GTG)5 for further evaluation. Afterwards, we applied this technique to 245 strains, and compared the results with the identification obtained by partial sequencing of the LSU rRNA gene, considered as the gold standard. An array matrix was constructed for each dataset and used as input for clustering with two methods (hierarchical dendrograms and QAPGrid layout). For both yeast datasets, unrelated species were clustered in the same group. The sensitivity score of (GTG)5 MSP-PCR fingerprinting was high, but specificity was low. As a conclusion, the yeast diversity inferred in several previous studies may have been underestimated and some isolates were probably misidentified due to the compliance to this screening procedure. |
publishDate |
2014 |
dc.date.issued.fl_str_mv |
2014 |
dc.date.accessioned.fl_str_mv |
2021-08-10T04:31:22Z |
dc.type.driver.fl_str_mv |
Estrangeiro info:eu-repo/semantics/article |
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info:eu-repo/semantics/publishedVersion |
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article |
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publishedVersion |
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http://hdl.handle.net/10183/225373 |
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1932-6203 |
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000938899 |
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http://hdl.handle.net/10183/225373 |
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eng |
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PLoS ONE. San Francisco. Vol. 9, no. 8 (Aug. 2014), e105870 [8] f. |
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info:eu-repo/semantics/openAccess |
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openAccess |
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