@ARTICLE{TreeBASE2Ref23701,
author = {Alexis L Carlson and Alfredo Justo and David S. Hibbett},
title = {Species delimitation in Trametes: a comparison of ITS, RPB1, RPB2 and TEF1 gene phylogenies },
year = {2014},
keywords = { gene phylogenies PolyPEET Polyporales systematics taxonomy},
doi = {},
url = {http://www.mycologia.org/content/106/4/735.abstract},
pmid = {},
journal = {Mycologia},
volume = {106},
number = {4},
pages = {735--745},
abstract = {Trametes is a cosmopolitan genus of white rot polypores, including the ?turkey tail? fungus, T. versicolor. Although Trametes is one of the most familiar genera of polypores, its species-level taxonomy is unsettled. The ITS region is the most commonly used molecular marker for species delimitation in fungi, but it has been shown to have a low molecular variation in Trametes resulting in poorly resolved phylogenies and unclear species boundaries, especially in the T. versicolor species complex (T. versicolor sensu stricto, T. ochracea, T. pubescens, T. ectypa). Here we evaluate the performance of three protein-coding genes (TEF1, RPB1, RPB2) for species delimitation and phylogenetic reconstruction in Trametes. We obtained 59 TEF1, 34 RPB1 and 55 RPB2 sequences from 69 individuals, focusing on the T. versicolor complex and performed phylogenetic analyses with maximum likelihood and parsimony methods. All three protein-coding genes outperformed ITS for separating species in the T. versicolor complex. The multigene phylogenetic analysis shows the highest amount of resolution and supported nodes separating T. ectypa, T. ochracea, T. pubescens and T. versicolor with strong support. In addition three slineages are resolved in the species complex of T. elegans. The T. elegans complex includes three species: T. elegans (based on material from Puerto Rico, Belize, the Philippines), T. aesculi (from North America) and T. repanda (from Papua New Guinea, the Philippines, Venezuela). The utility of gene markers varies, with TEF1 having the highest PCR and sequencing success rate and RPB1 offering the best backbone resolution for the genus. }
}
Citation for Study 14650
Citation title:
"Species delimitation in Trametes: a comparison of ITS, RPB1, RPB2 and TEF1 gene phylogenies ".
Study name:
"Species delimitation in Trametes: a comparison of ITS, RPB1, RPB2 and TEF1 gene phylogenies ".
This study is part of submission 14650
(Status: Published).
Citation
Carlson A.L., Justo A., & Hibbett D. 2014. Species delimitation in Trametes: a comparison of ITS, RPB1, RPB2 and TEF1 gene phylogenies. Mycologia, 106(4): 735-745.
Authors
-
Carlson A.L.
-
Justo A.
(submitter)
-
Hibbett D.
Abstract
Trametes is a cosmopolitan genus of white rot polypores, including the ?turkey tail? fungus, T. versicolor. Although Trametes is one of the most familiar genera of polypores, its species-level taxonomy is unsettled. The ITS region is the most commonly used molecular marker for species delimitation in fungi, but it has been shown to have a low molecular variation in Trametes resulting in poorly resolved phylogenies and unclear species boundaries, especially in the T. versicolor species complex (T. versicolor sensu stricto, T. ochracea, T. pubescens, T. ectypa). Here we evaluate the performance of three protein-coding genes (TEF1, RPB1, RPB2) for species delimitation and phylogenetic reconstruction in Trametes. We obtained 59 TEF1, 34 RPB1 and 55 RPB2 sequences from 69 individuals, focusing on the T. versicolor complex and performed phylogenetic analyses with maximum likelihood and parsimony methods. All three protein-coding genes outperformed ITS for separating species in the T. versicolor complex. The multigene phylogenetic analysis shows the highest amount of resolution and supported nodes separating T. ectypa, T. ochracea, T. pubescens and T. versicolor with strong support. In addition three slineages are resolved in the species complex of T. elegans. The T. elegans complex includes three species: T. elegans (based on material from Puerto Rico, Belize, the Philippines), T. aesculi (from North America) and T. repanda (from Papua New Guinea, the Philippines, Venezuela). The utility of gene markers varies, with TEF1 having the highest PCR and sequencing success rate and RPB1 offering the best backbone resolution for the genus.
Keywords
gene phylogenies PolyPEET Polyporales systematics taxonomy
External links
About this resource
- Canonical resource URI:
http://purl.org/phylo/treebase/phylows/study/TB2:S14650
- Other versions:
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- Show BibTeX reference
@ARTICLE{TreeBASE2Ref23701,
author = {Alexis L Carlson and Alfredo Justo and David S. Hibbett},
title = {Species delimitation in Trametes: a comparison of ITS, RPB1, RPB2 and TEF1 gene phylogenies },
year = {2014},
keywords = { gene phylogenies PolyPEET Polyporales systematics taxonomy},
doi = {},
url = {http://www.mycologia.org/content/106/4/735.abstract},
pmid = {},
journal = {Mycologia},
volume = {106},
number = {4},
pages = {735--745},
abstract = {Trametes is a cosmopolitan genus of white rot polypores, including the ?turkey tail? fungus, T. versicolor. Although Trametes is one of the most familiar genera of polypores, its species-level taxonomy is unsettled. The ITS region is the most commonly used molecular marker for species delimitation in fungi, but it has been shown to have a low molecular variation in Trametes resulting in poorly resolved phylogenies and unclear species boundaries, especially in the T. versicolor species complex (T. versicolor sensu stricto, T. ochracea, T. pubescens, T. ectypa). Here we evaluate the performance of three protein-coding genes (TEF1, RPB1, RPB2) for species delimitation and phylogenetic reconstruction in Trametes. We obtained 59 TEF1, 34 RPB1 and 55 RPB2 sequences from 69 individuals, focusing on the T. versicolor complex and performed phylogenetic analyses with maximum likelihood and parsimony methods. All three protein-coding genes outperformed ITS for separating species in the T. versicolor complex. The multigene phylogenetic analysis shows the highest amount of resolution and supported nodes separating T. ectypa, T. ochracea, T. pubescens and T. versicolor with strong support. In addition three slineages are resolved in the species complex of T. elegans. The T. elegans complex includes three species: T. elegans (based on material from Puerto Rico, Belize, the Philippines), T. aesculi (from North America) and T. repanda (from Papua New Guinea, the Philippines, Venezuela). The utility of gene markers varies, with TEF1 having the highest PCR and sequencing success rate and RPB1 offering the best backbone resolution for the genus. }
}
- Show RIS reference
TY - JOUR
ID - 23701
AU - Carlson,Alexis L
AU - Justo,Alfredo
AU - Hibbett,David S.
T1 - Species delimitation in Trametes: a comparison of ITS, RPB1, RPB2 and TEF1 gene phylogenies
PY - 2014
KW - gene phylogenies PolyPEET Polyporales systematics taxonomy
UR - http://www.mycologia.org/content/106/4/735.abstract
N2 - Trametes is a cosmopolitan genus of white rot polypores, including the ?turkey tail? fungus, T. versicolor. Although Trametes is one of the most familiar genera of polypores, its species-level taxonomy is unsettled. The ITS region is the most commonly used molecular marker for species delimitation in fungi, but it has been shown to have a low molecular variation in Trametes resulting in poorly resolved phylogenies and unclear species boundaries, especially in the T. versicolor species complex (T. versicolor sensu stricto, T. ochracea, T. pubescens, T. ectypa). Here we evaluate the performance of three protein-coding genes (TEF1, RPB1, RPB2) for species delimitation and phylogenetic reconstruction in Trametes. We obtained 59 TEF1, 34 RPB1 and 55 RPB2 sequences from 69 individuals, focusing on the T. versicolor complex and performed phylogenetic analyses with maximum likelihood and parsimony methods. All three protein-coding genes outperformed ITS for separating species in the T. versicolor complex. The multigene phylogenetic analysis shows the highest amount of resolution and supported nodes separating T. ectypa, T. ochracea, T. pubescens and T. versicolor with strong support. In addition three slineages are resolved in the species complex of T. elegans. The T. elegans complex includes three species: T. elegans (based on material from Puerto Rico, Belize, the Philippines), T. aesculi (from North America) and T. repanda (from Papua New Guinea, the Philippines, Venezuela). The utility of gene markers varies, with TEF1 having the highest PCR and sequencing success rate and RPB1 offering the best backbone resolution for the genus.
L3 -
JF - Mycologia
VL - 106
IS - 4
SP - 735
EP - 745
ER -