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Logo of bmcpsBioMed Centralsearchsubmit a manuscriptregisterthis articleBMC Plant Biology
 
BMC Plant Biol. 2012; 12: 53.
Published online Apr 21, 2012. doi:  10.1186/1471-2229-12-53
PMCID: PMC3349559
Transcriptome analysis of stem development in the tumourous stem mustard Brassica juncea var. tumida Tsen et Lee by RNA sequencing
Quan Sun,1 Guanfan Zhou,2 Yingfan Cai,corresponding author1 Yonghong Fan,2 Xiaoyan Zhu,1,3 Yihua Liu,2 Xiaohong He,1 Jinjuan Shen,2 Huaizhong Jiang,1 Daiwen Hu,2 Zheng Pan,1 Liuxin Xiang,1 Guanghua He,3 Daiwen Dong,2 and Jianping Yang1
1College of Bioinformation, Chongqing University of Posts and Telecommunications, Chongqing 400065, China
2Institute of Chongqing Fuling Agricultural Sciences, Fuling 408000, China
3Chongqing Key Laboratory of Application and Safety Control of Genetically Modified Crops, Southwest University, Chongqing 400716, China
corresponding authorCorresponding author.
Quan Sun: sunquan/at/cqupt.edu.cn; Guanfan Zhou: zgfan1208/at/163.com; Yingfan Cai: caiyf3000/at/yahoo.com.cn; Yonghong Fan: cqflfyh88/at/163.com; Xiaoyan Zhu: zhuxy/at/cqupt.edu.cn; Yihua Liu: liuyihua/at/cqupt.edu.cn; Xiaohong He: hexh/at/cqupt.edu.cn; Jinjuan Shen: shenjj/at/cqupt.edu.cn; Huaizhong Jiang: jianghz/at/cqupt.edu.cn; Daiwen Hu: hudw/at/cqupt.edu.cn; Zheng Pan: Panzheng/at/cqupt.edu.cn; Liuxin Xiang: xianglx/at/cqupt.edu.cn; Guanghua He: hegh/at/swu.edu.cn; Daiwen Dong: caiyf/at/cqupt.edu.cn; Jianping Yang: yangjianping/at/caas.net.cn
Received December 31, 2011; Accepted April 21, 2012.
Abstract
Background
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.
Results
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.
Conclusions
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.
Keywords: Transcriptome, Tumourous stem mustard, Development, RNA sequencing, Brassica juncea var. tumida
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