Abstract
BackgroundThe 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.ResultsRNA-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.ConclusionsThe 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.
Highlights
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
Generation, mapping, and assessment of RNA sequencing (RNA-seq) reads Paired-end RNA-seq reads of 90 bp in length were generated from six major organs or tissues of B. rapa including root, stem, leaf, flower, silique and callus
For eliminating the errors from the mis-priming of primers in RNA-seq experiments, the first nine base pairs of reads were trimmed before read alignment
Summary
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. 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. The species Brassica rapa (2n=20, AA) includes several subspecies providing human nutrition in the form of leafy, root and stem vegetables and edible oil It represents the origin of the Brassica ‘A’ genome and contributes to other cultivated oilseed crops of Brassica allopolyploids: B. napus (AACC) and B. juncea (AABB) [1]. With the availability of the B. rapa genome sequence [6], it is essential to further identify and determine the activity of all functional elements on a genome-wide scale For this purpose, a comprehensive analysis of the transcriptome is required to reveal potentially transcribed regions and understand expression patterns of the entire B. rapa gene model sets across tissues. RNA-seq data show a high level of reproducibility in both technical and biological replicates [14]
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a call
