RNA-Seq Analysis of Transcriptome and Glucosinolate Metabolism in Seeds and Sprouts of Broccoli (Brassica oleracea var. italic)

Abstract

BackgroundBroccoli (Brassica oleracea var. italica), a member of Cruciferae, is an important vegetable containing high concentration of various nutritive and functional molecules especially the anticarcinogenic glucosinolates. The sprouts of broccoli contain 10–100 times higher level of glucoraphanin, the main contributor of the anticarcinogenesis, than the edible florets. Despite the broccoli sprouts’ functional importance, currently available genetic and genomic tools for their studies are very limited, which greatly restricts the development of this functionally important vegetable.ResultsA total of ∼85 million 251 bp reads were obtained. After de novo assembly and searching the assembled transcripts against the Arabidopsis thaliana and NCBI nr databases, 19,441 top-hit transcripts were clustered as unigenes with an average length of 2,133 bp. These unigenes were classified according to their putative functional categories. Cluster analysis of total unigenes with similar expression patterns and differentially expressed unigenes among different tissues, as well as transcription factor analysis were performed. We identified 25 putative glucosinolate metabolism genes sharing 62.04–89.72% nucleotide sequence identity with the Arabidopsis orthologs. This established a broccoli glucosinolate metabolic pathway with high colinearity to Arabidopsis. Many of the biosynthetic and degradation genes showed higher expression after germination than in seeds; especially the expression of the myrosinase TGG2 was 20–130 times higher. These results along with the previous reports about these genes’ studies in Arabidopsis and the glucosinolate concentration in broccoli sprouts indicate the breakdown products of glucosinolates may play important roles in the stage of broccoli seed germination and sprout development.ConclusionOur study provides the largest genetic resource of broccoli to date. These data will pave the way for further studies and genetic engineering of broccoli sprouts and will also provide new insight into the genomic research of this species and its relatives.

De Novo Transcriptome Analysis of Plant Pathogenic Fungus Myrothecium roridum and Identification of Genes Associated with Trichothecene Mycotoxin Biosynthesis

“…The cDNA library was sequenced on the Illumina sequencing platform (Illumina HiSeq™ 2000, Illumina, San Diego, CA, USA) using the single-end paired-end technology in a single run. The original image processes of sequencing, base-calling, and quality value calculation were performed by the Illumina GA Pipeline (version 1.6, Illumina, San Diego, CA, USA), in which 90-bp paired-end reads were obtained [20,21]. …”

Differentially expressed genes and phenotypic variation in florets among the isogenic Ogura-CMS, DGMS and inbred lines of broccoli

“…For example, small RNA-Seq has revealed DEGs in the early development of broccoli pollen [19], and transcriptome analyses have been used to examine four transcription factors in normal and abortive buds of an Ogura-CMS line and its maintainer line [12]. In addition, the roles of pigment mechanisms in post-harvest broccoli yellowing [20], gene expression patterns associated with sulforaphane metabolism in broccoli orets [21], glucosinolate metabolism in seeds and sprouts [22,23], and yield heterosis in curds of broccoli have also been elucidated by RNA-Seq technology [24]. To the best of our knowledge, it would be the rst report of comparative transcriptome analyses of isogenic Ogura-CMS, DGMS and inbred lines in broccoli orets.…”

A Weighted Mean Value Analysis to Identify Biological Pathway Activity Changes during Poplar Seed Germination

“…italica Planch.) seed germination, Gao et al (2014) [11] identified 25 putative glucosinolate metabolism-related genes, which shared 62.04%-89.72% nucleotide sequence identity with the Arabidopsis orthologs. In particular, the expression level of myrosinase TGG2 after germination was 20-130 times greater than in dry seeds.…”