title: Transcriptome analysis of stem development in the tumourous stem mustard Brassica juncea var. tumida Tsen et Lee by RNA sequencing.
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.
authors.affiliation: College of Bioinformation, Chongqing University of Posts and Telecommunications, Chongqing 400065, China.
authors.forename: Quan
authors.initials: Q
authors.lastname: Sun
authors.forename: Guanfan
authors.initials: G
authors.lastname: Zhou
authors.forename: Yingfan
authors.initials: Y
authors.lastname: Cai
authors.forename: Yonghong
authors.initials: Y
authors.lastname: Fan
authors.forename: Xiaoyan
authors.initials: X
authors.lastname: Zhu
authors.forename: Yihua
authors.initials: Y
authors.lastname: Liu
authors.forename: Xiaohong
authors.initials: X
authors.lastname: He
authors.forename: Jinjuan
authors.initials: J
authors.lastname: Shen
authors.forename: Huaizhong
authors.initials: H
authors.lastname: Jiang
authors.forename: Daiwen
authors.initials: D
authors.lastname: Hu
authors.forename: Zheng
authors.initials: Z
authors.lastname: Pan
authors.forename: Liuxin
authors.initials: L
authors.lastname: Xiang
authors.forename: Guanghua
authors.initials: G
authors.lastname: He
authors.forename: Daiwen
authors.initials: D
authors.lastname: Dong
authors.forename: Jianping
authors.initials: J
authors.lastname: Yang
mesh_terms: D020869:Gene Expression Profiling / Q000379:methods*; D018506:Gene Expression Regulation, Plant; D009149:Mustard Plant / Q000235:genetics* / Q000254:growth & development; D018547:Plant Stems / Q000235:genetics* / Q000254:growth & development; D017423:Sequence Analysis, RNA / Q000379:methods*