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

Abstract

BackgroundTumourous 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.ResultsUsing 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.ConclusionsOur 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.

Development of PR genes panel for screening aphid-tolerant cultivars in Brassica juncea

“…Hence, fast and more accurate detection methods for measuring the basal defense responses in breeding progenies has to be used in combination with visual parameters of screening for resistance in hybrid breeding programs. In the present study, expression of 14 defense-responsive genes assimilated from studies of Taj et al (2011), Bhardwaj et al (2015 and Sun et al (2012) was quantified in stem, leaf and pod sections of GM 3 variety of mustard (Brassica juncea) sampled from an aphid-infested field located at Pethapur, Gandhinagar, Gujarat. Non-infested stem, leaf and pod sections were taken as calibrator control samples during relative quantitation study with ACT3 gene as the endogenous control.…”

“…Distances Mediates cross talk between JA signaling and auxin biosynthesis to regulate lateral root formation Sun et al (2012) 14 HSFA7A1 Heat shock factor A7A1 Highly expressed during high temperature stress conditions Bhardwaj et al (2015) 15 ACT3 Actin Ubiquitous component of plant cytoskeleton. Involved in cell division, plane localization, cell elongation and cell shape determination Sun et al (2012) between samples and assays are calculated for hierarchical clustering based on the DCT values using pearson's correlation distance. Heat map portrays the expression of the 14 pathogen-responsive genes; the color scale illustrates the relative expression level of pathogen-responsive genes, representing DCT.…”

“…All the primers used in the study for the development of PR genes panel were selected from the works of Taj et al (2011), Bhardwaj et al (2015 and Sun et al (2012) (Table 1). Primer sequences of all the genes used in the panel development study are furnished in Table 2.…”

Erratum to: Transcriptome analysis of stem development in the tumourous stem mustard Brassica juncea var. tumidaTsen et Lee by RNA sequencing

“…After the publication of our study [1], we became aware of errors in the proofreading of the article that caused a description mistake in the experimental methods section. These mistakes do not affect the final information in the analysis and results.…”

Applications and challenges of next-generation sequencing in Brassica species

“…The transcriptome of tumourous stem mustard (B. juncea var. tumida Tsen et Lee) was sequenced by Illumina short-read technology, identifying 146,265 unigenes, in which 1,042 significantly expressed genes were associated with stem swelling and development (Sun et al 2012). Zhou et al (2011b) identified 7,155 genes related to chloroplast development in B. oleracea, determined the role of regulatory genes by RNA sequencing with the Illumina Genome Analyzer II system, and discovered 1,600 up-regulated genes in light signaling pathways in green curd tissue.…”