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Open Access Highly Accessed Research article

Comprehensive analysis of RNA-seq data reveals the complexity of the transcriptome in Brassica rapa

Chaobo Tong1, Xiaowu Wang2, Jingyin Yu1, Jian Wu2, Wanshun Li3, Junyan Huang1, Caihua Dong1, Wei Hua1* and Shengyi Liu1*

Author Affiliations

1 Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, P.R. China, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan 430062, China

2 Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, P.R. China, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 10081, China

3 Beijing Genome Institute-Shenzhen, Shenzhen 518083, China

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BMC Genomics 2013, 14:689  doi:10.1186/1471-2164-14-689

Published: 7 October 2013

Abstract

Background

The species Brassica rapa (2n=20, AA) is an important vegetable and oilseed crop, and serves as an excellent model for genomic and evolutionary research in Brassica species. With the availability of whole genome sequence of B. rapa, it is essential to further determine the activity of all functional elements of the B. rapa genome and explore the transcriptome on a genome-wide scale. Here, RNA-seq data was employed to provide a genome-wide transcriptional landscape and characterization of the annotated and novel transcripts and alternative splicing events across tissues.

Results

RNA-seq reads were generated using the Illumina platform from six different tissues (root, stem, leaf, flower, silique and callus) of the B. rapa accession Chiifu-401-42, the same line used for whole genome sequencing. First, these data detected the widespread transcription of the B. rapa genome, leading to the identification of numerous novel transcripts and definition of 5'/3' UTRs of known genes. Second, 78.8% of the total annotated genes were detected as expressed and 45.8% were constitutively expressed across all tissues. We further defined several groups of genes: housekeeping genes, tissue-specific expressed genes and co-expressed genes across tissues, which will serve as a valuable repository for future crop functional genomics research. Third, alternative splicing (AS) is estimated to occur in more than 29.4% of intron-containing B. rapa genes, and 65% of them were commonly detected in more than two tissues. Interestingly, genes with high rate of AS were over-represented in GO categories relating to transcriptional regulation and signal transduction, suggesting potential importance of AS for playing regulatory role in these genes. Further, we observed that intron retention (IR) is predominant in the AS events and seems to preferentially occurred in genes with short introns.

Conclusions

The high-resolution RNA-seq analysis provides a global transcriptional landscape as a complement to the B. rapa genome sequence, which will advance our understanding of the dynamics and complexity of the B. rapa transcriptome. The atlas of gene expression in different tissues will be useful for accelerating research on functional genomics and genome evolution in Brassica species.

Keywords:
Brassica rapa; RNA-seq; Alternative splicing; Transcriptome