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

Ming-Ju Amy Lyu,Gane Ka-Shu Wong,Udo Gowik,Steve Kelly,Matt Stata,Sarah Covshoff,Xin-Guang Zhu,Rowan F Sage,Xiaofeng Wei,Julia Mallmann,Julian M Hibberd,Peter Westhoff,Haorong Lu

doi:10.1186/s12862-015-0399-9

Abstract

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.Electronic supplementary materialThe online version of this article (doi:10.1186/s12862-015-0399-9) contains supplementary material, which is available to authorized users.

Highlights

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
Overview of RNA-Seq samples sequenced through Illumina platform To construct a phylogenetic tree of the genus Flaveria, we obtained Illumina RNA-Seq data from 17 Flaveria species (3 C3, 4 C4, 7 C3-C4 and 3 C4-like intermediate species) and 3 out-group species from the Asteraceae (Table 1)
The results showed that, the topology of the phylogenetic tree of 16 Flaveria species based on singleton reference coding sequences (CDS) (s-CDS) (Additional file 4) was identical to that based on minimal reference coding sequences (m-CDS) (Fig. 4)

Summary

Introduction

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. C4 photosynthesis evolved repeatedly from C3 photosynthesis in at least 66 different lineages of angiosperms [1, 2] Many of these evolutionary transitions are coincident with the decline of atmospheric CO2 concentration in the Oligocene [1, 3, 4]. Because of the C4 photosynthetic pathway, C4 plants are able to concentrate CO2 into the bundle sheath cells (BSC) where RuBisCO (ribulose 1,5bisphosphate carboxylase/oxygenase) is localized [5]. This substantially reduces the inhibitory process of photorespiration and increases light, water and nitrogen use efficiencies in C4 relative to C3 plants [6, 7].

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