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

• Published in: BMC plant biology Vol. 12; no. 1; p. 53
• Main Authors: Sun, Quan, Zhou, Guanfan, Cai, Yingfan, Fan, Yonghong, Zhu, Xiaoyan, Liu, Yihua, He, Xiaohong, Shen, Jinjuan, Jiang, Huaizhong, Hu, Daiwen, Pan, Zheng, Xiang, Liuxin, He, Guanghua, Dong, Daiwen, Yang, Jianping
• Format: Journal Article
• Language: English
• Published: London BioMed Central 21.04.2012; BioMed Central Ltd; BMC
• Subjects: Agriculture; Biomedical and Life Sciences; Brassica; Brassica juncea var. tumida; Comparative analysis; Data processing; Development; Developmental stages; DNA sequencing; Experiments; Gene expression; Gene Expression Profiling - methods; Gene Expression Regulation, Plant; Genes; Genetic aspects; Genetic transcription; Genetically altered foods; Genetics; Genomics; Growth; Life Sciences; Mustard Plant - genetics; Mustard Plant - growth & development; Nucleotide sequencing; Plant Sciences; Plant Stems - genetics; Plant Stems - growth & development; Raw materials; Research Article; RNA; RNA sequencing; Sequence Analysis, RNA - methods; Signal transduction; Studies; Technological change; Transcriptome; Tree Biology; Tumors; Tumourous stem mustard; Vegetables; China; Tumourous stem mustard; RNA sequencing; Development; var; Transcriptome
• ISSN: 1471-2229; 1471-2229
• DOI: 10.1186/1471-2229-12-53

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.