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

BMC Evolutionary Biology

Research Article

Haorong Lu¹  Xiaofeng Wei¹  Gane Ka-Shu Wong²  Xin-Guang Zhu³  Ming-Ju Amy Lyu³  Matt Stata⁴  Rowan F. Sage⁴  Sarah Covshoff⁵  Julian M. Hibberd⁵  Steve Kelly⁶  Julia Mallmann⁷  Peter Westhoff⁷  Udo Gowik⁷ 

[1] BGI-Shenzhen, Beishan Industrial Zone, Yantian District, 518083, Shenzhen, China;BGI-Shenzhen, Beishan Industrial Zone, Yantian District, 518083, Shenzhen, China;Department of Biological Sciences, University of Alberta, T6G 2E9, Edmonton, AB, Canada;Department of Medicine, University of Alberta, T6G 2E1, Edmonton, AB, Canada;CAS-MPG Partner Institute and Key Laboratory for Computational Biology, Shanghai Institutes for Biological Sciences, Shanghai, China;Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Canada;Department of Plant Sciences, University of Cambridge, Cambridge, UK;Department of Plant Sciences, University of Oxford, Oxford, UK;Institute of Plant Molecular and Developmental Biology, Heinrich-Heine-University, Dusseldorf, Germany;

关键词: Flaveria;    RNA-Seq;    Phylogenetic tree;    C photosynthesis;   

DOI  :  10.1186/s12862-015-0399-9

 received in 2014-12-04, accepted in 2015-05-29,  发布年份 2015

来源: Springer

【 摘 要 】

BackgroundThe genus Flaveria has been extensively used as a model to study the evolution of C4 photosynthesis as it contains C3 and C4 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).ResultsHere 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 (C3) and F. angustifolia (C3-C4).ConclusionsWe 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 C4 photosynthesis in the Flavaria clade.

【 授权许可】

Unknown   
© 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.