@ARTICLE{TreeBASE2Ref25612,
author = {Melvin R Duvall and Amanda E. Fisher and J. Travis Columbus and Amanda L. Ingram and William P. Wysocki and Sean Vincent Burke and Lynn Clark and Scot A. Kelchner},
title = {Phylogenomics and plastome evolution of the chloridoid grasses (Chloridoideae; Poaceae)},
year = {2016},
keywords = {Poaceae, full plastome, Chloridoideae},
doi = {10.1086/684526},
url = {http://},
pmid = {},
journal = {International Journal of Plant Sciences},
volume = {177},
number = {3},
pages = {},
abstract = {Premise of research. Studies of complete plastomes have proven informative for our understanding of the
molecular evolution and phylogenomics of grasses, but subfamily Chloridoideae has not been included in this
research. In previous multilocus studies, specific deep branches, as in the large clade corresponding to Cyno-
donteae, are not uniformly well supported.
Methodology. In this study, a plastome phylogenomic analysis sampled 14 species representing 4 tribes
and 10 genera of Chloridoideae. One species was Sanger sequenced, and 14 other species, including out-
groups, were sequenced with next-generation sequencing-by-synthesis methods. Plastomes from next-generation
sequences were assembled by de novo methods, and the unambiguously aligned coding and noncoding se-
quences of the entire plastomes were analyzed phylogenetically.
Pivotal results. Chloridoid plastomes showed rare genomic changes in Distichlis, Centropodia, and
Eragrostis tef that were of potential phylogenomic significance. Phylogenomic analyses showed uniformly
strong support for all ingroup relationships except one node in Cynodonteae in which a short internal branch
connected long terminal branches. Resolution within this clade was found to be taxon dependent and possibly
subject to long-branch attraction artifacts.
Conclusions. Our study indicates that the increase in phylogenetic information in sequences of entire
plastomes well resolves and strongly supports relationships among tribes and genera of chloridoid grasses.
Sampling more species, especially in the Centropodia + Ellisochloa clade and Cynodonteae, will further ad-
dress relationships in these groups and clarify the evolutionary origins of the subfamily.}
}
Citation for Study 18944
Citation title:
"Phylogenomics and plastome evolution of the chloridoid grasses (Chloridoideae; Poaceae)".
Study name:
"Phylogenomics and plastome evolution of the chloridoid grasses (Chloridoideae; Poaceae)".
This study is part of submission 18944
(Status: Published).
Citation
Duvall M.R., Fisher A.E., Columbus J., Ingram A.L., Wysocki W.P., Burke S.V., Clark L., & Kelchner S. 2016. Phylogenomics and plastome evolution of the chloridoid grasses (Chloridoideae; Poaceae). International Journal of Plant Sciences, 177(3).
Authors
-
Duvall M.R.
-
Fisher A.E.
-
Columbus J.
-
Ingram A.L.
7653616389
-
Wysocki W.P.
(submitter)
630-433-8282
-
Burke S.V.
-
Clark L.
-
Kelchner S.
Abstract
Premise of research. Studies of complete plastomes have proven informative for our understanding of the
molecular evolution and phylogenomics of grasses, but subfamily Chloridoideae has not been included in this
research. In previous multilocus studies, specific deep branches, as in the large clade corresponding to Cyno-
donteae, are not uniformly well supported.
Methodology. In this study, a plastome phylogenomic analysis sampled 14 species representing 4 tribes
and 10 genera of Chloridoideae. One species was Sanger sequenced, and 14 other species, including out-
groups, were sequenced with next-generation sequencing-by-synthesis methods. Plastomes from next-generation
sequences were assembled by de novo methods, and the unambiguously aligned coding and noncoding se-
quences of the entire plastomes were analyzed phylogenetically.
Pivotal results. Chloridoid plastomes showed rare genomic changes in Distichlis, Centropodia, and
Eragrostis tef that were of potential phylogenomic significance. Phylogenomic analyses showed uniformly
strong support for all ingroup relationships except one node in Cynodonteae in which a short internal branch
connected long terminal branches. Resolution within this clade was found to be taxon dependent and possibly
subject to long-branch attraction artifacts.
Conclusions. Our study indicates that the increase in phylogenetic information in sequences of entire
plastomes well resolves and strongly supports relationships among tribes and genera of chloridoid grasses.
Sampling more species, especially in the Centropodia + Ellisochloa clade and Cynodonteae, will further ad-
dress relationships in these groups and clarify the evolutionary origins of the subfamily.
Keywords
Poaceae, full plastome, Chloridoideae
External links
About this resource
- Canonical resource URI:
http://purl.org/phylo/treebase/phylows/study/TB2:S18944
- Other versions:
Nexus
NeXML
- Show BibTeX reference
@ARTICLE{TreeBASE2Ref25612,
author = {Melvin R Duvall and Amanda E. Fisher and J. Travis Columbus and Amanda L. Ingram and William P. Wysocki and Sean Vincent Burke and Lynn Clark and Scot A. Kelchner},
title = {Phylogenomics and plastome evolution of the chloridoid grasses (Chloridoideae; Poaceae)},
year = {2016},
keywords = {Poaceae, full plastome, Chloridoideae},
doi = {10.1086/684526},
url = {http://},
pmid = {},
journal = {International Journal of Plant Sciences},
volume = {177},
number = {3},
pages = {},
abstract = {Premise of research. Studies of complete plastomes have proven informative for our understanding of the
molecular evolution and phylogenomics of grasses, but subfamily Chloridoideae has not been included in this
research. In previous multilocus studies, specific deep branches, as in the large clade corresponding to Cyno-
donteae, are not uniformly well supported.
Methodology. In this study, a plastome phylogenomic analysis sampled 14 species representing 4 tribes
and 10 genera of Chloridoideae. One species was Sanger sequenced, and 14 other species, including out-
groups, were sequenced with next-generation sequencing-by-synthesis methods. Plastomes from next-generation
sequences were assembled by de novo methods, and the unambiguously aligned coding and noncoding se-
quences of the entire plastomes were analyzed phylogenetically.
Pivotal results. Chloridoid plastomes showed rare genomic changes in Distichlis, Centropodia, and
Eragrostis tef that were of potential phylogenomic significance. Phylogenomic analyses showed uniformly
strong support for all ingroup relationships except one node in Cynodonteae in which a short internal branch
connected long terminal branches. Resolution within this clade was found to be taxon dependent and possibly
subject to long-branch attraction artifacts.
Conclusions. Our study indicates that the increase in phylogenetic information in sequences of entire
plastomes well resolves and strongly supports relationships among tribes and genera of chloridoid grasses.
Sampling more species, especially in the Centropodia + Ellisochloa clade and Cynodonteae, will further ad-
dress relationships in these groups and clarify the evolutionary origins of the subfamily.}
}
- Show RIS reference
TY - JOUR
ID - 25612
AU - Duvall,Melvin R
AU - Fisher,Amanda E.
AU - Columbus,J. Travis
AU - Ingram,Amanda L.
AU - Wysocki,William P.
AU - Burke,Sean Vincent
AU - Clark,Lynn
AU - Kelchner,Scot A.
T1 - Phylogenomics and plastome evolution of the chloridoid grasses (Chloridoideae; Poaceae)
PY - 2016
KW - Poaceae
KW - full plastome
KW - Chloridoideae
UR - http://dx.doi.org/10.1086/684526
N2 - Premise of research. Studies of complete plastomes have proven informative for our understanding of the
molecular evolution and phylogenomics of grasses, but subfamily Chloridoideae has not been included in this
research. In previous multilocus studies, specific deep branches, as in the large clade corresponding to Cyno-
donteae, are not uniformly well supported.
Methodology. In this study, a plastome phylogenomic analysis sampled 14 species representing 4 tribes
and 10 genera of Chloridoideae. One species was Sanger sequenced, and 14 other species, including out-
groups, were sequenced with next-generation sequencing-by-synthesis methods. Plastomes from next-generation
sequences were assembled by de novo methods, and the unambiguously aligned coding and noncoding se-
quences of the entire plastomes were analyzed phylogenetically.
Pivotal results. Chloridoid plastomes showed rare genomic changes in Distichlis, Centropodia, and
Eragrostis tef that were of potential phylogenomic significance. Phylogenomic analyses showed uniformly
strong support for all ingroup relationships except one node in Cynodonteae in which a short internal branch
connected long terminal branches. Resolution within this clade was found to be taxon dependent and possibly
subject to long-branch attraction artifacts.
Conclusions. Our study indicates that the increase in phylogenetic information in sequences of entire
plastomes well resolves and strongly supports relationships among tribes and genera of chloridoid grasses.
Sampling more species, especially in the Centropodia + Ellisochloa clade and Cynodonteae, will further ad-
dress relationships in these groups and clarify the evolutionary origins of the subfamily.
L3 - 10.1086/684526
JF - International Journal of Plant Sciences
VL - 177
IS - 3
ER -
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