title: RNA-Seq based phylogeny recapitulates previous phylogeny of the genus Flaveria (Asteraceae) with some modifications.
abstract: BACKGROUND
  The 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).
  
  
  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 (C3) and F. angustifolia (C3-C4).
  
  
  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 C4 photosynthesis in the Flavaria clade.
authors.affiliation: CAS-MPG Partner Institute and Key Laboratory for Computational Biology, Shanghai Institutes for Biological Sciences, Shanghai, China. mingju.lv@gmail.com.
authors.forename: Ming-Ju Amy
authors.initials: MJ
authors.lastname: Lyu
authors.affiliation: Institute of Plant Molecular and Developmental Biology, Heinrich-Heine-University, Dusseldorf, Germany. gowik@uni-duesseldorf.de.
authors.forename: Udo
authors.initials: U
authors.lastname: Gowik
authors.affiliation: Department of Plant Sciences, University of Oxford, Oxford, UK. steven.kelly@plants.ox.ac.uk.
authors.forename: Steve
authors.initials: S
authors.lastname: Kelly
authors.affiliation: Department of Plant Sciences, University of Cambridge, Cambridge, UK. sarahcovshoff@gmail.com.
authors.forename: Sarah
authors.initials: S
authors.lastname: Covshoff
authors.affiliation: Institute of Plant Molecular and Developmental Biology, Heinrich-Heine-University, Dusseldorf, Germany. julia.mallmann@uni-duesseldorf.de.
authors.forename: Julia
authors.initials: J
authors.lastname: Mallmann
authors.affiliation: Institute of Plant Molecular and Developmental Biology, Heinrich-Heine-University, Dusseldorf, Germany. west@uni-duesseldorf.de.
authors.forename: Peter
authors.initials: P
authors.lastname: Westhoff
authors.affiliation: Department of Plant Sciences, University of Cambridge, Cambridge, UK. jmh65@cam.ac.uk.
authors.forename: Julian M
authors.initials: JM
authors.lastname: Hibberd
authors.affiliation: Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Canada. mattstata@gmail.com.
authors.forename: Matt
authors.initials: M
authors.lastname: Stata
authors.affiliation: Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Canada. r.sage@utoronto.ca.
authors.forename: Rowan F
authors.initials: RF
authors.lastname: Sage
authors.affiliation: BGI-Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen, 518083, China. luhaorong@genomics.cn.
authors.forename: Haorong
authors.initials: H
authors.lastname: Lu
authors.affiliation: BGI-Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen, 518083, China. weixiaofeng@genomics.cn.
authors.forename: Xiaofeng
authors.initials: X
authors.lastname: Wei
authors.affiliation: BGI-Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen, 518083, China. gane@ualberta.ca.|Department of Biological Sciences, University of Alberta, Edmonton, AB, T6G 2E9, Canada. gane@ualberta.ca.|Department of Medicine, University of Alberta, Edmonton, AB, T6G 2E1, Canada. gane@ualberta.ca.
authors.forename: Gane Ka-Shu
authors.initials: GK
authors.lastname: Wong
authors.affiliation: CAS-MPG Partner Institute and Key Laboratory for Computational Biology, Shanghai Institutes for Biological Sciences, Shanghai, China. xinguang.zhu@gmail.com.
authors.forename: Xin-Guang
authors.initials: XG
authors.lastname: Zhu
mesh_terms: D000595:Amino Acid Sequence; D005075:Biological Evolution; D002736:Chloroplasts / Q000235:genetics; D037142:Flaveria / Q000145:classification* / Q000235:genetics* / Q000502:physiology; D010788:Photosynthesis; D010802:Phylogeny; D018749:RNA, Plant / Q000032:analysis; D017423:Sequence Analysis, RNA / Q000379:methods
chemical_list: D018749:RNA, Plant