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E-GEOD-54339 - RNA-Seq Based Reconstruction of the Phylogenetic Tree of the Genus Flaveria (Asteraceae)

Status
Released on 8 January 2015, last updated on 12 March 2015
Organism
Flaveria angustifolia, Flaveria bidentis, Flaveria brownii, Flaveria cronquistii, Flaveria kochiana, Flaveria palmeri, Flaveria pringlei, Flaveria pubescens, Flaveria sonorensis, Flaveria trinervia, Flaveria vaginata, Helenium autumnale, Tanacetum parthenium, Tragopogon dubius
Samples (21)
Protocols (4)
Description
The genus Flaveria has been extensively used as a model to study the evolution of C4 photosynthesis as it contains both C3 and C4 species as well as a number of species that exhibit intermediate types of photosynthesis. The current phylogenetic tree of the Flaveria genus contains 21 of the 23 known Flaveria species and has been constructed using a combination of morphologicial data and three non-coding DNA sequences (nuclear encoded ETS, ITS and chloroplast encoded trnl-F). However, recent studies have suggested that phylogenetic trees inferred using a small number of molecular sequences may often be incorrect. Moreover, studies in other genera have often shown substantial differences between trees inferred using morphological data and those using molecular sequence. To provide new insight into the phylogeny of the genus Flaveria we utilize RNA-Seq data to construct a multi-gene concatenated phylogenetic tree of 17 Flaveria species. Furthermore, we use this new data to identify 14 C4 specific non-synonymous mutation sites, 12 of which (86%) can be independently verified by public sequence data. We propose that the data collection method provided in this study can be used as a generic method for facilitating phylogenetic tree reconstruction in the absence of reference genomes for the target species. 18 Flaveria sample including 11 species are sequenced, other three samples were also sequenced as out-group. In all, 21 samples.
Experiment type
RNA-seq of coding RNA 
Contacts
Ming Ju Lu <amypicb@126.com>, Gane K Wong, Ming-Ju A Lv, Sarah Covshoff, Xin-Guang Zhu
MINSEQE
Exp. designProtocolsVariablesProcessedSeq. reads
Files
Investigation descriptionE-GEOD-54339.idf.txt
Sample and data relationshipE-GEOD-54339.sdrf.txt
Additional data (1)E-GEOD-54339.additional.1.zip
Links