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Citation for Study 20782

Citation title: "Evaluating multi-locus phylogenies for species boundaries determination in the genus Diaporthe".

Study name: "Evaluating multi-locus phylogenies for species boundaries determination in the genus Diaporthe".

This study is part of submission 20782 (Status: Published).

Citation

Santos L., Alves A., & Alves R. 2017. Evaluating multi-locus phylogenies for species boundaries determination in the genus Diaporthe. PeerJ, .

Authors

Santos L.
Alves A. (submitter) 00351234370970
Alves R.

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 multiloci 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 four loci treeas almost equivalent to the five 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.

Keywords

Diaporthe, Phylogeny, Maximum likelihood, Maximum parsimony, Phomopsis, Multi-locus

External links

DOI: 10.7717/peerj.3120

About this resource

Canonical resource URI: http://purl.org/phylo/treebase/phylows/study/TB2:S20782
Other versions: Nexus NeXML

Show BibTeX reference

		@ARTICLE{TreeBASE2Ref27029,
	 author = {Liliana  Santos and Artur  Alves and Rui  Alves},
	 title = {Evaluating multi-locus phylogenies for species boundaries determination in the genus Diaporthe},
	 year = {2017},
	 keywords = {Diaporthe, Phylogeny, Maximum likelihood, Maximum parsimony, Phomopsis, Multi-locus},
	 doi = {10.7717/peerj.3120},
	 url = {http://},
	 pmid = {},
	 journal = {PeerJ},
	 volume = {},
	 number = {},
	 pages = {},
	 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 multiloci
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 four loci treeas almost equivalent to the five 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.}
}

Show RIS reference

TY - JOUR
ID - 27029
AU - Santos,Liliana
AU - Alves,Artur
AU - Alves,Rui
T1 - Evaluating multi-locus phylogenies for species boundaries determination in the genus Diaporthe
PY - 2017
KW - Diaporthe
KW - Phylogeny
KW - Maximum likelihood
KW - Maximum parsimony
KW - Phomopsis
KW - Multi-locus
UR - http://dx.doi.org/10.7717/peerj.3120
N2 - 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 multiloci
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 four loci treeas almost equivalent to the five 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.
L3 - 10.7717/peerj.3120
JF - PeerJ
VL -
IS -
ER -