Improving ITS sequence data for identification of plant pathogenic fungi
Autor(a) principal: | |
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Data de Publicação: | 2014 |
Outros Autores: | , , , , , , , , , , , , , , , , |
Tipo de documento: | Artigo |
Idioma: | eng |
Título da fonte: | LOCUS Repositório Institucional da UFV |
Texto Completo: | http://dx.doi.org/10.1007/s13225-014-0291-8 http://www.locus.ufv.br/handle/123456789/22292 |
Resumo: | Plant pathogenic fungi are a large and diverse assemblage of eukaryotes with substantial impacts on natural ecosystems and human endeavours. These taxa often have complex and poorly understood life cycles, lack observable, discriminatory morphological characters, and may not be amenable to in vitro culturing. As a result, species identification is frequently difficult. Molecular (DNA sequence) data have emerged as crucial information for the taxonomic identification of plant pathogenic fungi, with the nuclear ribosomal internal transcribed spacer (ITS) region being the most popular marker. However, international nucleotide sequence databases are accumulating numerous sequences of compromised or low-resolution taxonomic annotations and substandard technical quality, making their use in the molecular identification of plant pathogenic fungi problematic. Here we report on a concerted effort to identify high-quality reference sequences for various plant pathogenic fungi and to re-annotate incorrectly or insufficiently annotated public ITS sequences from these fungal lineages. A third objective was to enrich the sequences with geographical and ecological metadata. The results – a total of 31,954 changes – are incorporated in and made available through the UNITE database for molecular identification of fungi (http://unite.ut.ee), including standalone FASTA files of sequence data for local BLAST searches, use in the next-generation sequencing analysis platforms QIIME and mothur, and related applications. The present initiative is just a beginning to cover the wide spectrum of plant pathogenic fungi, and we invite all researchers with pertinent expertise to join the annotation effort. |
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Pereira, Olinto LipariniPinho, Danilo BatistaNilsson, R. HenrikHyde, Kevin D.Pawłowska, JuliaRyberg, MartinTedersoo, LehoAas, Anders BjørnsgardAlias, Siti A.Alves, ArturAnderson, Cajsa LisaAntonelli, AlexandreArnold, A. ElizabethBahnmann, BarbaraBahram, MohammadBengtsson-Palme, JohanBerlin, Annaet al.2018-10-16T17:41:19Z2018-10-16T17:41:19Z2014-05-1518789129http://dx.doi.org/10.1007/s13225-014-0291-8http://www.locus.ufv.br/handle/123456789/22292Plant pathogenic fungi are a large and diverse assemblage of eukaryotes with substantial impacts on natural ecosystems and human endeavours. These taxa often have complex and poorly understood life cycles, lack observable, discriminatory morphological characters, and may not be amenable to in vitro culturing. As a result, species identification is frequently difficult. Molecular (DNA sequence) data have emerged as crucial information for the taxonomic identification of plant pathogenic fungi, with the nuclear ribosomal internal transcribed spacer (ITS) region being the most popular marker. However, international nucleotide sequence databases are accumulating numerous sequences of compromised or low-resolution taxonomic annotations and substandard technical quality, making their use in the molecular identification of plant pathogenic fungi problematic. Here we report on a concerted effort to identify high-quality reference sequences for various plant pathogenic fungi and to re-annotate incorrectly or insufficiently annotated public ITS sequences from these fungal lineages. A third objective was to enrich the sequences with geographical and ecological metadata. The results – a total of 31,954 changes – are incorporated in and made available through the UNITE database for molecular identification of fungi (http://unite.ut.ee), including standalone FASTA files of sequence data for local BLAST searches, use in the next-generation sequencing analysis platforms QIIME and mothur, and related applications. The present initiative is just a beginning to cover the wide spectrum of plant pathogenic fungi, and we invite all researchers with pertinent expertise to join the annotation effort.engFungal Diversityv. 67, n. 1, p. 11– 19, jul. 2014Springer Nature Switzerland AG.info:eu-repo/semantics/openAccessPhytopathogenic fungiMolecular identificationITSTaxonomyAnnotationImproving ITS sequence data for identification of plant pathogenic fungiinfo:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articleapplication/pdfreponame:LOCUS Repositório Institucional da UFVinstname:Universidade Federal de Viçosa (UFV)instacron:UFVORIGINALartigo.pdfartigo.pdftexto completoapplication/pdf971927https://locus.ufv.br//bitstream/123456789/22292/1/artigo.pdfc20baccc82732d81e77f61053948cae3MD51LICENSElicense.txtlicense.txttext/plain; charset=utf-81748https://locus.ufv.br//bitstream/123456789/22292/2/license.txt8a4605be74aa9ea9d79846c1fba20a33MD52123456789/222922018-10-16 14:42:52.329oai:locus.ufv.br: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Repositório InstitucionalPUBhttps://www.locus.ufv.br/oai/requestfabiojreis@ufv.bropendoar:21452018-10-16T17:42:52LOCUS Repositório Institucional da UFV - Universidade Federal de Viçosa (UFV)false |
dc.title.en.fl_str_mv |
Improving ITS sequence data for identification of plant pathogenic fungi |
title |
Improving ITS sequence data for identification of plant pathogenic fungi |
spellingShingle |
Improving ITS sequence data for identification of plant pathogenic fungi Pereira, Olinto Liparini Phytopathogenic fungi Molecular identification ITS Taxonomy Annotation |
title_short |
Improving ITS sequence data for identification of plant pathogenic fungi |
title_full |
Improving ITS sequence data for identification of plant pathogenic fungi |
title_fullStr |
Improving ITS sequence data for identification of plant pathogenic fungi |
title_full_unstemmed |
Improving ITS sequence data for identification of plant pathogenic fungi |
title_sort |
Improving ITS sequence data for identification of plant pathogenic fungi |
author |
Pereira, Olinto Liparini |
author_facet |
Pereira, Olinto Liparini Pinho, Danilo Batista Nilsson, R. Henrik Hyde, Kevin D. Pawłowska, Julia Ryberg, Martin Tedersoo, Leho Aas, Anders Bjørnsgard Alias, Siti A. Alves, Artur Anderson, Cajsa Lisa Antonelli, Alexandre Arnold, A. Elizabeth Bahnmann, Barbara Bahram, Mohammad Bengtsson-Palme, Johan Berlin, Anna et al. |
author_role |
author |
author2 |
Pinho, Danilo Batista Nilsson, R. Henrik Hyde, Kevin D. Pawłowska, Julia Ryberg, Martin Tedersoo, Leho Aas, Anders Bjørnsgard Alias, Siti A. Alves, Artur Anderson, Cajsa Lisa Antonelli, Alexandre Arnold, A. Elizabeth Bahnmann, Barbara Bahram, Mohammad Bengtsson-Palme, Johan Berlin, Anna et al. |
author2_role |
author author author author author author author author author author author author author author author author author |
dc.contributor.author.fl_str_mv |
Pereira, Olinto Liparini Pinho, Danilo Batista Nilsson, R. Henrik Hyde, Kevin D. Pawłowska, Julia Ryberg, Martin Tedersoo, Leho Aas, Anders Bjørnsgard Alias, Siti A. Alves, Artur Anderson, Cajsa Lisa Antonelli, Alexandre Arnold, A. Elizabeth Bahnmann, Barbara Bahram, Mohammad Bengtsson-Palme, Johan Berlin, Anna et al. |
dc.subject.pt-BR.fl_str_mv |
Phytopathogenic fungi Molecular identification ITS Taxonomy Annotation |
topic |
Phytopathogenic fungi Molecular identification ITS Taxonomy Annotation |
description |
Plant pathogenic fungi are a large and diverse assemblage of eukaryotes with substantial impacts on natural ecosystems and human endeavours. These taxa often have complex and poorly understood life cycles, lack observable, discriminatory morphological characters, and may not be amenable to in vitro culturing. As a result, species identification is frequently difficult. Molecular (DNA sequence) data have emerged as crucial information for the taxonomic identification of plant pathogenic fungi, with the nuclear ribosomal internal transcribed spacer (ITS) region being the most popular marker. However, international nucleotide sequence databases are accumulating numerous sequences of compromised or low-resolution taxonomic annotations and substandard technical quality, making their use in the molecular identification of plant pathogenic fungi problematic. Here we report on a concerted effort to identify high-quality reference sequences for various plant pathogenic fungi and to re-annotate incorrectly or insufficiently annotated public ITS sequences from these fungal lineages. A third objective was to enrich the sequences with geographical and ecological metadata. The results – a total of 31,954 changes – are incorporated in and made available through the UNITE database for molecular identification of fungi (http://unite.ut.ee), including standalone FASTA files of sequence data for local BLAST searches, use in the next-generation sequencing analysis platforms QIIME and mothur, and related applications. The present initiative is just a beginning to cover the wide spectrum of plant pathogenic fungi, and we invite all researchers with pertinent expertise to join the annotation effort. |
publishDate |
2014 |
dc.date.issued.fl_str_mv |
2014-05-15 |
dc.date.accessioned.fl_str_mv |
2018-10-16T17:41:19Z |
dc.date.available.fl_str_mv |
2018-10-16T17:41:19Z |
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/10.1007/s13225-014-0291-8 http://www.locus.ufv.br/handle/123456789/22292 |
dc.identifier.issn.none.fl_str_mv |
18789129 |
identifier_str_mv |
18789129 |
url |
http://dx.doi.org/10.1007/s13225-014-0291-8 http://www.locus.ufv.br/handle/123456789/22292 |
dc.language.iso.fl_str_mv |
eng |
language |
eng |
dc.relation.ispartofseries.pt-BR.fl_str_mv |
v. 67, n. 1, p. 11– 19, jul. 2014 |
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Springer Nature Switzerland AG. info:eu-repo/semantics/openAccess |
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Springer Nature Switzerland AG. |
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openAccess |
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Fungal Diversity |
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Fungal Diversity |
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