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Transcriptome analysis of stem development in the tumourous stem mustard Brassica juncea var. tumida Tsen et Lee by RNA sequencing

Quan Sun1, Guanfan Zhou2, Yingfan Cai1*, Yonghong Fan2, Xiaoyan Zhu13, Yihua Liu2, Xiaohong He1, Jinjuan Shen2, Huaizhong Jiang1, Daiwen Hu2, Zheng Pan1, Liuxin Xiang1, Guanghua He3, Daiwen Dong2 and Jianping Yang1

Author Affiliations

1 College of Bioinformation, Chongqing University of Posts and Telecommunications, Chongqing 400065, China

2 Institute of Chongqing Fuling Agricultural Sciences, Fuling 408000, China

3 Chongqing Key Laboratory of Application and Safety Control of Genetically Modified Crops, Southwest University, Chongqing 400716, China

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BMC Plant Biology 2012, 12:53  doi:10.1186/1471-2229-12-53

Published: 21 April 2012



Tumourous stem mustard (Brassica juncea var. tumida Tsen et Lee) is an economically and nutritionally important vegetable crop of the Cruciferae family that also provides the raw material for Fuling mustard. The genetics breeding, physiology, biochemistry and classification of mustards have been extensively studied, but little information is available on tumourous stem mustard at the molecular level. To gain greater insight into the molecular mechanisms underlying stem swelling in this vegetable and to provide additional information for molecular research and breeding, we sequenced the transcriptome of tumourous stem mustard at various stem developmental stages and compared it with that of a mutant variety lacking swollen stems.


Using Illumina short-read technology with a tag-based digital gene expression (DGE) system, we performed de novo transcriptome assembly and gene expression analysis. In our analysis, we assembled genetic information for tumourous stem mustard at various stem developmental stages. In addition, we constructed five DGE libraries, which covered the strains Yong'an and Dayejie at various development stages. Illumina sequencing identified 146,265 unigenes, including 11,245 clusters and 135,020 singletons. The unigenes were subjected to a BLAST search and annotated using the GO and KO databases. We also compared the gene expression profiles of three swollen stem samples with those of two non-swollen stem samples. A total of 1,042 genes with significantly different expression levels occurring simultaneously in the six comparison groups were screened out. Finally, the altered expression levels of a number of randomly selected genes were confirmed by quantitative real-time PCR.


Our data provide comprehensive gene expression information at the transcriptional level and the first insight into the understanding of the molecular mechanisms and regulatory pathways of stem swelling and development in this plant, and will help define new mechanisms of stem development in non-model plant organisms.

Transcriptome; Tumourous stem mustard; Development; RNA sequencing; Brassica juncea var. tumida