RNA-seq analysis of transcriptome and glucosinolate metabolism in seeds and sprouts of broccoli (Brassica oleracea var. italic)

PLoS One. 2014 Feb 27;9(2):e88804. doi: 10.1371/journal.pone.0088804. eCollection 2014.


Background: Broccoli (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.

Results: A 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.

Conclusion: Our 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.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Brassica / genetics*
  • Brassica / metabolism*
  • Cluster Analysis
  • Computational Biology
  • Databases, Genetic
  • Gene Expression Profiling
  • Glucosinolates / metabolism*
  • High-Throughput Nucleotide Sequencing
  • Metabolic Networks and Pathways
  • Molecular Sequence Annotation
  • Seeds / genetics*
  • Seeds / metabolism*
  • Transcription Factors / genetics
  • Transcriptome*


  • Glucosinolates
  • Transcription Factors

Grant support

The national Natural Science Foundation of China 31370334 http://www.nsfc.gov.cn/Portal0/default152.htm; Opening project of Key Laboratory of breed improvement and physiecology of cold region crops, College of Heilongjiang Province; Heilongjiang Provincial University Science and Technology Innovation Team Building Program 2011TD005; The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.