Comparative Transcriptional Profiling Provides Insights into the Evolution and Development of the Zygomorphic Flower of Vicia sativa (Papilionoideae)

Abstract

Background Vicia sativa (the common vetch) possesses a predominant zygomorphic flower and belongs to the subfamily Papilionoideae, which is related to Arabidopsis thaliana in the eurosid II clade of the core eudicots. Each vetch flower consists of 21 concentrically arranged organs: the outermost five sepals, then five petals and ten stamens, and a single carpel in the center.Methodology/Principal Findings We explored the floral transcriptome to examine a genome-scale genetic model of the zygomorphic flower of vetch. mRNA was obtained from an equal mixture of six floral organs, leaves and roots. De novo assembly of the vetch transcriptome using Illumina paired-end technology produced 71,553 unigenes with an average length of 511 bp. We then compared the expression changes in the 71,553 unigenes in the eight independent organs through RNA-Seq Quantification analysis. We predominantly analyzed gene expression patterns specific to each floral organ and combinations of floral organs that corresponded to the traditional ABC model domains. Comparative analyses were performed in the floral transcriptomes of vetch and Arabidopsis, and genomes of vetch and Medicago truncatula.Conclusions/Significance Our comparative analysis of vetch and Arabidopsis showed that the vetch flowers conform to a strict ABC model. We analyzed the evolution and expression of the TCP gene family in vetch at a whole-genome level, and several unigenes specific to three different vetch petals, which might offer some clues toward elucidating the molecular mechanisms underlying floral zygomorphy. Our results provide the first insights into the genome-scale molecular regulatory network that controls the evolution and development of the zygomorphic flower in Papilionoideae.

Peer Review #1 of "Development of polymorphic EST-SSR markers and characterization of the autotetraploid genome of sainfoin (Onobrychis viciifolia) (v0.1)"

“…Our GO enrichment analysis showed that unigenes related to the category "transcription" were significantly enriched. This finding agreed with our previous investigations on alfalfa and Vicia sativa using similar GO analyses of SSR-containing unigene approaches (Liu et al, 2013a;Liu et al, 2013b). The results of GO enrichment analysis of unigenes containing EST-SSR loci indicated that EST-SSR loci are not randomly distributed in the transcriptome and it preference exists in transcription factors (Fig S5C).…”

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“…Our GO enrichment analysis showed that unigenes related to the category "transcription" were significantly enriched. This finding agreed with our previous investigations on alfalfa and Vicia sativa using similar GO analyses of SSR-containing unigene approaches (Liu et al, 2013a;Liu et al, 2013b) and indicated that the "transcription"-related unigenes are likely to contain more SSR repeats than other unigenes (Luo et al, 2015).…”

Transcriptome and small RNA combined sequencing analysis of cold tolerance response in non-heading Chinese cabbage

“…As a convenient tool for transcriptome analysis, RNA-Seq, has been increasingly targeted at species that do not have access to genomic sequences [53][54][55]. Here, we used RNA-Seq to measure gene expression levels in non-heading Chinese cabbage different varieties and under low temperature treatment.…”