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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 phylogenies. However, defining the op...
Autores principales: | , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
PeerJ Inc.
2017
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5372842/ https://www.ncbi.nlm.nih.gov/pubmed/28367371 http://dx.doi.org/10.7717/peerj.3120 |
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author | Santos, Liliana Alves, Artur Alves, Rui |
author_facet | Santos, Liliana Alves, Artur Alves, Rui |
author_sort | Santos, Liliana |
collection | PubMed |
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 phylogenies. 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. |
format | Online Article Text |
id | pubmed-5372842 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2017 |
publisher | PeerJ Inc. |
record_format | MEDLINE/PubMed |
spelling | pubmed-53728422017-03-31 Evaluating multi-locus phylogenies for species boundaries determination in the genus Diaporthe Santos, Liliana Alves, Artur Alves, Rui PeerJ Microbiology 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 phylogenies. 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. PeerJ Inc. 2017-03-28 /pmc/articles/PMC5372842/ /pubmed/28367371 http://dx.doi.org/10.7717/peerj.3120 Text en ©2017 Santos et al. http://creativecommons.org/licenses/by/4.0/ This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, reproduction and adaptation in any medium and for any purpose provided that it is properly attributed. For attribution, the original author(s), title, publication source (PeerJ) and either DOI or URL of the article must be cited. |
spellingShingle | Microbiology Santos, Liliana Alves, Artur Alves, Rui 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 |
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_short | 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 |
topic | Microbiology |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5372842/ https://www.ncbi.nlm.nih.gov/pubmed/28367371 http://dx.doi.org/10.7717/peerj.3120 |
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