Evaluating multi-locus phylogenies for species boundaries determination in the genus Diaporthe

Background. Species identification is essential for controlling disease, understanding epidemiology, and to guide the implementation of phytosanitary measures against fungi from the genus Diaporthe. Accurate Diaporthe species separation requires using multi loci phylogernes. However, defining the op...

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Autores: Santos, Liliana, Alves, Artur, Alves, Rui
Formato: artículo
Estado:Versión publicada
Fecha de publicación:2017
País:España
Recursos:Universitat de Lleida (UdL)
Repositorio:Repositori Obert UdL
OAI Identifier:oai:repositori.udl.cat:10459.1/59867
Acesso em linha:https://doi.org/10.7717/peerj.3120
http://hdl.handle.net/10459.1/59867
Access Level:acceso abierto
Palavra-chave:Microbiologia
Biologia molecular
Micologia
Microbiology
Molecular biology
Mycology
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spelling Evaluating multi-locus phylogenies for species boundaries determination in the genus DiaportheSantos, LilianaAlves, ArturAlves, RuiMicrobiologiaBiologia molecularMicologiaMicrobiologyMolecular biologyMycologyBackground. Species identification is essential for controlling disease, understanding epidemiology, and to guide the implementation of phytosanitary measures against fungi from the genus Diaporthe. Accurate Diaporthe species separation requires using multi loci phylogernes. However, defining the optimal set of loci that can be used for species identification is still an open problem. Methods. Here we addressed that problem by identifying five loci that have been sequenced in 142 Diaporthe isolates representing 96 species: TEF1, TUB, CAL, HIS and ITS. We then used every possible combination of those loci to build, analyse, and compare phylogenetic trees. Results. As expected, species separation is better when all five loci are simultaneously used to build the phylogeny of the isolates. However, removing the ITS locus has little effect on reconstructed phylogenies, identifying the TEF1-TUB-CAL-HIS 4-loci tree as almost equivalent to the 5-loci tree. We further identify the best 3-loci, 2-loci, and 1-locus trees that should be used for species separation in the genus. Discussion. Our results question the current use of the ITS locus for DNA barcoding in the genus Diaporthe and suggest that TEF1 might be a better choice if one locus barcoding needs to be done.This work was financed by European Funds through COMPETE and by National Funds through the Portuguese Foundation for Science and Technology (FCT) within project PANDORA (PTDC/AGR-FOR/3807/2012 –FCOMP-01-0124-FEDER-027979). The authors received financing from FCT to CESAM (UID/AMB/50017/2013), Artur Alves (FCT Investigator Programme –IF/00835/2013) and a post-doctoral grant to Liliana Santos (SFRH/BPD/90684/2012), grants BFU2010-17704 from Ministerio de Ciencia e Innovación, 2009SGR809 from Generalitat de Catalunya, and bridge grants from the Dean for Research and the Departament de Ciències Mèdiques Bàsiques of the University of Lleida (Spain) to Rui Alves.Peerj2017info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionapplication/pdfhttps://doi.org/10.7717/peerj.3120http://hdl.handle.net/10459.1/59867reponame:Repositori Obert UdL instname:Universitat de Lleida (UdL)Inglésinfo:eu-repo/grantAgreement/MICINN//BFU2010-17704Reproducció del document publicat a: https://doi.org/10.7717/peerj.3120Peerj, 2017, vol. 5, num. e3120cc-by (c) Santos, Liliana et al., 2017info:eu-repo/semantics/openAccesshttp://creativecommons.org/licenses/by/3.0/esoai:repositori.udl.cat:10459.1/598672026-06-24T12:42:17Z
dc.title.none.fl_str_mv Evaluating multi-locus phylogenies for species boundaries determination in the genus Diaporthe
title Evaluating multi-locus phylogenies for species boundaries determination in the genus Diaporthe
spellingShingle Evaluating multi-locus phylogenies for species boundaries determination in the genus Diaporthe
Santos, Liliana
Microbiologia
Biologia molecular
Micologia
Microbiology
Molecular biology
Mycology
title_short Evaluating multi-locus phylogenies for species boundaries determination in the genus Diaporthe
title_full Evaluating multi-locus phylogenies for species boundaries determination in the genus Diaporthe
title_fullStr Evaluating multi-locus phylogenies for species boundaries determination in the genus Diaporthe
title_full_unstemmed Evaluating multi-locus phylogenies for species boundaries determination in the genus Diaporthe
title_sort Evaluating multi-locus phylogenies for species boundaries determination in the genus Diaporthe
dc.creator.none.fl_str_mv Santos, Liliana
Alves, Artur
Alves, Rui
author Santos, Liliana
author_facet Santos, Liliana
Alves, Artur
Alves, Rui
author_role author
author2 Alves, Artur
Alves, Rui
author2_role author
author
dc.subject.none.fl_str_mv Microbiologia
Biologia molecular
Micologia
Microbiology
Molecular biology
Mycology
topic Microbiologia
Biologia molecular
Micologia
Microbiology
Molecular biology
Mycology
description Background. Species identification is essential for controlling disease, understanding epidemiology, and to guide the implementation of phytosanitary measures against fungi from the genus Diaporthe. Accurate Diaporthe species separation requires using multi loci phylogernes. However, defining the optimal set of loci that can be used for species identification is still an open problem. Methods. Here we addressed that problem by identifying five loci that have been sequenced in 142 Diaporthe isolates representing 96 species: TEF1, TUB, CAL, HIS and ITS. We then used every possible combination of those loci to build, analyse, and compare phylogenetic trees. Results. As expected, species separation is better when all five loci are simultaneously used to build the phylogeny of the isolates. However, removing the ITS locus has little effect on reconstructed phylogenies, identifying the TEF1-TUB-CAL-HIS 4-loci tree as almost equivalent to the 5-loci tree. We further identify the best 3-loci, 2-loci, and 1-locus trees that should be used for species separation in the genus. Discussion. Our results question the current use of the ITS locus for DNA barcoding in the genus Diaporthe and suggest that TEF1 might be a better choice if one locus barcoding needs to be done.
publishDate 2017
dc.date.none.fl_str_mv 2017
dc.type.none.fl_str_mv info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
format article
status_str publishedVersion
dc.identifier.none.fl_str_mv https://doi.org/10.7717/peerj.3120
http://hdl.handle.net/10459.1/59867
url https://doi.org/10.7717/peerj.3120
http://hdl.handle.net/10459.1/59867
dc.language.none.fl_str_mv Inglés
language_invalid_str_mv Inglés
dc.relation.none.fl_str_mv info:eu-repo/grantAgreement/MICINN//BFU2010-17704
Reproducció del document publicat a: https://doi.org/10.7717/peerj.3120
Peerj, 2017, vol. 5, num. e3120
dc.rights.none.fl_str_mv cc-by (c) Santos, Liliana et al., 2017
info:eu-repo/semantics/openAccess
http://creativecommons.org/licenses/by/3.0/es
rights_invalid_str_mv cc-by (c) Santos, Liliana et al., 2017
http://creativecommons.org/licenses/by/3.0/es
eu_rights_str_mv openAccess
dc.format.none.fl_str_mv application/pdf
dc.publisher.none.fl_str_mv Peerj
publisher.none.fl_str_mv Peerj
dc.source.none.fl_str_mv reponame:Repositori Obert UdL
instname:Universitat de Lleida (UdL)
instname_str Universitat de Lleida (UdL)
reponame_str Repositori Obert UdL
collection Repositori Obert UdL
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repository.mail.fl_str_mv
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