Genome-Wide Transcriptome Analysis of the Reference Brassica rapa chiifu-402-401

After the draft Brassiuca rapa chiifu-401 genome has been publised in last year, it becomes essential to further massively identify and determine the transcriptional activity of all the functional elements in B.rapa genome. Currently RNA-seq provides a powerful and cost-efficient tool for investigating and understanding the dynamics of transcriptome at single base resolution. We present the transcriptome atlas for six organs (root, stem, leaf, flower, silique, callus) of B.rapa reference accession chiifu-401. Using high-throughput paired-end RNA-seq, we unambiguously detected transcripts expressing at an extremely low level, as well as a substantial number of novel transcripts, exons, and 5’/3’UTRs. We also identified significant constitutively expressed, co-expressed and tissue-specific expressed genes in multiple tissues, which will serve as a valuable resource for candidate functional gene in B.rapa. At least 36.5% of intron-containing B.rapa genes are estimated to be alternatively spliced by RNA-seq data. Intron retention is the most common event and seems to be related to shorter intron size. AS genes are enriched in “regulation”,“binding”-related GO catergories, and ocurred preferentially in organ-specific pattern, which play an important role in regulating gene expression and generating tissue specificity. We also observed that ? % of alternative splicing transcripts introduced frame shifts or produced premature termination codons (PTC), indicating that the corresponding transcripts could be potential candidates for NMD. Taken together, the comprehensive investigation of the B.rapa transcriptome extensively improved genome annotation and unveil the complex gene transcription and regulation. These transcriptome profile and expression value for each gene will be useful and valuable for further research of gene expression, function and evolution.