The activation of gene expression and alternative splicing in the formation and evolution of allopolyploid Brassica napus

Allopolyploids contain two or more sets of subgenomes. To establish a compatible relationship between subgenomes, a series of gene expression changes has occurred in allopolyploids. What evolutionary changes have taken place in transcripts of Brassica napus during its early establishment and subsequent evolution is a fascinating scientific question. Here, we study this issue using a set of materials (natural and resynthesized B. napus and their progenitors/parents) and long-read RNA sequencing technology. The results showed that more genes were upregulated in resynthesized B. napus compared with its two parents, and more upregulated expressed genes were observed in natural B. napus than in resynthesized B. napus. The presence of upregulated genes in an organism may help it to adapt to the influence of “genomic shock” and cope with the natural environment. Isoforms are produced from precursor mRNAs by alternative splicing (AS) events, and more than 60% of the isoforms identified in all materials were novel, potentially improving the reference genome information for B. napus. We found that the isoform numbers and the numbers of genes potentially involved in AS and alternative polyadenylation increased in B. napus after evolution, and they may have been involved in the adaptation of plants to the natural environment. In addition, all identified isoforms were functionally annotated by searching seven databases. In general, this study can improve our overall understanding of the full-length transcriptome of B. napus and help us to recognize the significant changes in gene expression and isoform abundance that have occurred in allopolyploid B. napus during evolution.