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RNA-Seq based phylogeny recapitulates previous phylogeny of the genus Flaveria (Asteraceae) with some modifications

BACKGROUND: The genus Flaveria has been extensively used as a model to study the evolution of C(4) photosynthesis as it contains C(3) and C(4) species as well as a number of species that exhibit intermediate types of photosynthesis. The current phylogenetic tree of the genus Flaveria contains 21 of...

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Autores principales: Lyu, Ming-Ju Amy, Gowik, Udo, Kelly, Steve, Covshoff, Sarah, Mallmann, Julia, Westhoff, Peter, Hibberd, Julian M., Stata, Matt, Sage, Rowan F., Lu, Haorong, Wei, Xiaofeng, Wong, Gane Ka-Shu, Zhu, Xin-Guang
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2015
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4472175/
https://www.ncbi.nlm.nih.gov/pubmed/26084484
http://dx.doi.org/10.1186/s12862-015-0399-9
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author Lyu, Ming-Ju Amy
Gowik, Udo
Kelly, Steve
Covshoff, Sarah
Mallmann, Julia
Westhoff, Peter
Hibberd, Julian M.
Stata, Matt
Sage, Rowan F.
Lu, Haorong
Wei, Xiaofeng
Wong, Gane Ka-Shu
Zhu, Xin-Guang
author_facet Lyu, Ming-Ju Amy
Gowik, Udo
Kelly, Steve
Covshoff, Sarah
Mallmann, Julia
Westhoff, Peter
Hibberd, Julian M.
Stata, Matt
Sage, Rowan F.
Lu, Haorong
Wei, Xiaofeng
Wong, Gane Ka-Shu
Zhu, Xin-Guang
author_sort Lyu, Ming-Ju Amy
collection PubMed
description BACKGROUND: The genus Flaveria has been extensively used as a model to study the evolution of C(4) photosynthesis as it contains C(3) and C(4) species as well as a number of species that exhibit intermediate types of photosynthesis. The current phylogenetic tree of the genus Flaveria contains 21 of the 23 known Flaveria species and has been previously constructed using a combination of morphological data and three non-coding DNA sequences (nuclear encoded ETS, ITS and chloroplast encoded trnL-F). RESULTS: Here we developed a new strategy to update the phylogenetic tree of 16 Flaveria species based on RNA-Seq data. The updated phylogeny is largely congruent with the previously published tree but with some modifications. We propose that the data collection method provided in this study can be used as a generic method for phylogenetic tree reconstruction if the target species has no genomic information. We also showed that a “F. pringlei” genotype recently used in a number of labs may be a hybrid between F. pringlei (C(3)) and F. angustifolia (C(3)-C(4)). CONCLUSIONS: We propose that the new strategy of obtaining phylogenetic sequences outlined in this study can be used to construct robust trees in a larger number of taxa. The updated Flaveria phylogenetic tree also supports a hypothesis of stepwise and parallel evolution of C(4) photosynthesis in the Flavaria clade. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12862-015-0399-9) contains supplementary material, which is available to authorized users.
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spelling pubmed-44721752015-06-19 RNA-Seq based phylogeny recapitulates previous phylogeny of the genus Flaveria (Asteraceae) with some modifications Lyu, Ming-Ju Amy Gowik, Udo Kelly, Steve Covshoff, Sarah Mallmann, Julia Westhoff, Peter Hibberd, Julian M. Stata, Matt Sage, Rowan F. Lu, Haorong Wei, Xiaofeng Wong, Gane Ka-Shu Zhu, Xin-Guang BMC Evol Biol Research Article BACKGROUND: The genus Flaveria has been extensively used as a model to study the evolution of C(4) photosynthesis as it contains C(3) and C(4) species as well as a number of species that exhibit intermediate types of photosynthesis. The current phylogenetic tree of the genus Flaveria contains 21 of the 23 known Flaveria species and has been previously constructed using a combination of morphological data and three non-coding DNA sequences (nuclear encoded ETS, ITS and chloroplast encoded trnL-F). RESULTS: Here we developed a new strategy to update the phylogenetic tree of 16 Flaveria species based on RNA-Seq data. The updated phylogeny is largely congruent with the previously published tree but with some modifications. We propose that the data collection method provided in this study can be used as a generic method for phylogenetic tree reconstruction if the target species has no genomic information. We also showed that a “F. pringlei” genotype recently used in a number of labs may be a hybrid between F. pringlei (C(3)) and F. angustifolia (C(3)-C(4)). CONCLUSIONS: We propose that the new strategy of obtaining phylogenetic sequences outlined in this study can be used to construct robust trees in a larger number of taxa. The updated Flaveria phylogenetic tree also supports a hypothesis of stepwise and parallel evolution of C(4) photosynthesis in the Flavaria clade. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12862-015-0399-9) contains supplementary material, which is available to authorized users. BioMed Central 2015-06-18 /pmc/articles/PMC4472175/ /pubmed/26084484 http://dx.doi.org/10.1186/s12862-015-0399-9 Text en © Lyu et al. 2015 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, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
spellingShingle Research Article
Lyu, Ming-Ju Amy
Gowik, Udo
Kelly, Steve
Covshoff, Sarah
Mallmann, Julia
Westhoff, Peter
Hibberd, Julian M.
Stata, Matt
Sage, Rowan F.
Lu, Haorong
Wei, Xiaofeng
Wong, Gane Ka-Shu
Zhu, Xin-Guang
RNA-Seq based phylogeny recapitulates previous phylogeny of the genus Flaveria (Asteraceae) with some modifications
title RNA-Seq based phylogeny recapitulates previous phylogeny of the genus Flaveria (Asteraceae) with some modifications
title_full RNA-Seq based phylogeny recapitulates previous phylogeny of the genus Flaveria (Asteraceae) with some modifications
title_fullStr RNA-Seq based phylogeny recapitulates previous phylogeny of the genus Flaveria (Asteraceae) with some modifications
title_full_unstemmed RNA-Seq based phylogeny recapitulates previous phylogeny of the genus Flaveria (Asteraceae) with some modifications
title_short RNA-Seq based phylogeny recapitulates previous phylogeny of the genus Flaveria (Asteraceae) with some modifications
title_sort rna-seq based phylogeny recapitulates previous phylogeny of the genus flaveria (asteraceae) with some modifications
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4472175/
https://www.ncbi.nlm.nih.gov/pubmed/26084484
http://dx.doi.org/10.1186/s12862-015-0399-9
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