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title Evaluating multi-locus phylogenies for species boundaries determination in the genus Diaporthe
authors Santos, L; Alves, A; Alves, R
author full name Santos, Liliana; Alves, Artur; Alves, Rui
title Evaluating multi-locus phylogenies for species boundaries determination in the genus Diaporthe
nationality internacional
source PEERJ
language English
document type Article
author keywords Diaporthe; Phylogeny; Maximum likelihood; Maximum parsimony; Phomopsis; Multi-locus
keywords plus INTERNAL TRANSCRIBED SPACER; STEM CANKER; NUCLEOTIDE SUBSTITUTIONS; COELOMYCETE PHOMOPSIS; METABOLIC NETWORKS; MITOCHONDRIAL-DNA; GENOME SEQUENCE; UNITED-STATES; CAUSAL AGENT; SEED DECAY
abstract 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.
author address [Santos, Liliana; Alves, Artur] Univ Aveiro, CESAM, Dept Biol, Aveiro, Portugal; [Alves, Rui] Univ Lleida, Dept Ciencies Med Basiques, Lleida, Spain; [Alves, Rui] IRBLleida, Lleida, Spain
reprint address Alves, A (reprint author), Univ Aveiro, CESAM, Dept Biol, Aveiro, Portugal.; Alves, R (reprint author), Univ Lleida, Dept Ciencies Med Basiques, Lleida, Spain.; Alves, R (reprint author), IRBLleida, Lleida, Spain.
e-mail address artur.alves@ua.pt; ralves@cmb.udl.cat
researcherid number Alves, Artur/C-3645-2008
orcid number Alves, Artur/0000-0003-0117-2958
funding agency and grant number European Funds through COMPETE; National Funds through the Portuguese Foundation for Science and Technology (FCT) within project PANDORA [PTDC/AGR-FOR/3807/2012 -FCOMP-01-0124-FEDER-027979]; FCT [UID/AMB/50017/2013]; Artur Alves [IF/00835/2013, SFRH/BPD/90684/2012]; Dean for Research and the Departament de Ciencies Mediques Basiques of the University of Lleida (Spain)
funding text 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 Innovacion, 2009SGR809 from Generalitat de Catalunya, and bridge grants from the Dean for Research and the Departament de Ciencies Mediques Basiques of the University of Lleida (Spain) to Rui Alves. There was no additional external funding received for this study. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
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cited reference count 76
publisher PEERJ INC
publisher city LONDON
publisher address 341-345 OLD ST, THIRD FLR, LONDON, EC1V 9LL, ENGLAND
issn 2167-8359
29-character source abbreviation PEERJ
iso source abbreviation PeerJ
publication date MAR 28
year published 2017
volume 5
article number e3120
digital object identifier (doi) 10.7717/peerj.3120
page count 26
web of science category Multidisciplinary Sciences
subject category Science & Technology - Other Topics
document delivery number EQ3LG
unique article identifier WOS:000397973200006
link http://dx.doi.org/10.7717/peerj.3120
autores membros do CESAM