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

ABSTRACT: RNA-Seq Based Reconstruction of the Phylogenetic Tree of the Genus Flaveria (Asteraceae)

PROVIDER: PRJNA236235 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR1141030_1.fastq.gz	Fastqsanger.gz
	SRR1141030_2.fastq.gz	Fastqsanger.gz
	SRR1141040_1.fastq.gz	Fastqsanger.gz
	SRR1141040_2.fastq.gz	Fastqsanger.gz
	SRR1141031_1.fastq.gz	Fastqsanger.gz

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

Project 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.

2015-01-08 | E-GEOD-54339 | biostudies-arrayexpress

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

2015-01-08 | GSE54339 | GEO

Asteraceae

Project description:Organelle Genomes of Asteraceae

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Asteraceae

Project description:Asteraceae Raw sequence reads

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Project description:Flaveria whole genome sequence

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Within-host diversity improves phylogenetic reconstruction of SARS-CoV-2 outbreaks

Project description:Within-host diversity improves phylogenetic reconstruction of SARS-CoV-2 outbreaks

| PRJEB53224 | ENA

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

Project description: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.

| S-EPMC4472175 | biostudies-literature

Flaveria trinervia

Project description:Flaveria trinervia Organism overview

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Flaveria bidentis

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Flaveria robusta

Project description:Flaveria robusta Organism overview

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