A global survey of the transcriptome of the allopolyploid Brassica napus based on single molecule long-read isoform sequencing and Illumina-based RNA-seq data.

Brassica napus is a recent allopolyploid derived from the hybridization of B. rapa (Ar Ar ) and B. oleracea (Co Co ). Because of the high sequence similarity between the An and Cn subgenomes, it is difficult to provide an accurate landscape of the whole transcriptome of B. napus. To overcome this problem, we applied a single-molecule long-read isoform sequencing (Iso-Seq) technique that can produce long reads to explore the complex transcriptome of B. napus at the isoform level. From the Iso-Seq data, we obtained 147,698 nonredundant isoforms, capturing 37,403 annotated genes. A total of 18.1% (14,934/82,367) of the multi-exonic genes showed alternative splicing (AS). In addition, we identified 549 long noncoding RNAs (lncRNAs), the majority of which displayed tissue-specific expression profiles, and detected 7,742 annotated genes that possessed isoforms containing alternative polyadenylation (APA) sites. Moreover, 31,591 AS events located in open reading frame (ORF) lead to potential protein isoforms by in-frame or frameshift changes in the ORF. Illumina RNA-seq of five tissues that were pooled for Iso-Seq was also performed and showed that 69% of the total AS events were tissue-specific. Our data provides abundant transcriptome resources for the transcript isoform catalog of B. napus, which will facilitate genome reannotation, strengthen our understanding of the B. napus transcriptome and be applied for further functional genomic research.