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

Abstract

Allopolyploids contain two or more sets of subgenomes. To establish a compatible relationship between subgenomes, a series of gene expression changes occurred in allopolyploids. What evolutionary changes of transcripts have taken place in Brassica napus during the early establishment and subsequent evolution was a fascinating scientific question. Here, we study this issue using a set of materials (natural, resynthesized B. napus and their progenitors/parents) by long-read RNA sequencing technology. The results showed that more genes were up-regulated in resynthesized B. napus compared with its two parents, and more up-regulated expressed genes were observed in natural B. napus compared with resynthesized B. napus. The presence of up-regulation genes in organism may help it adapt to the influence of “genomic shock” and cope with natural environment. Isoforms are produced from precursor mRNAs by alternative splicing (AS) events, and more than 60% of novel isoforms were identified in all materials, which could improve the reference genome information of B. napus. We found that the isoform numbers, the number of genes potentially involved in AS and alternative polyadenylation increased in B. napus after evolution, which may involve in the adaptation of plants to natural environment. In addition, all identified isoforms were functional annotated by searching 7 databases. In general, this study could improve our overall understanding of the full-length transcriptome of B. napus, and help us recognize the significant gene expression changes and isoform abundance changes occurred in allopolyploid B. napus during evolution.

Differential alternative splicing genes and isoform co-expression networks of Brassica napus under multiple abiotic stresses

“…A growing body of evidence have reported that SR protein encoding genes underwent AS events in response to environmental stresses in plants. For example, SR45a and RS2Z33 produced different isoforms to respond to drought stress in G. uralensis ( Li et al., 2022b ). A few SR genes were certificated to exhibit responsive AS patterns under heat, drought, and salt stress conditions in wheat ( Liu et al., 2018 ).…”

Asymmetric subgenomic chromatin architecture impacts on gene expression in resynthesized and natural allopolyploid Brassica napus

“…Third-generation sequencing libraries were constructed by using the same plant materials used for ATAC-Seq with three biological replicates. The process of constructing RNA-Seq libraries can be found in our previous study 6 . Raw RNA-Seq data were filtered (length > 100, quality >7) by NanoFilt (v.2.5.0) to generate clean data.…”

“…Polyploidization brings two or more sets of identical or distinct genomes into a nucleus, producing either autopolyploids or allopolyploids 3 , which is accompanied by dramatic and dynamic genetic and epigenetic changes 3 – 5 , and allopolyploids have long been thought to play a more critical role in plant divergence due to unique hybridization during their formation 4 . Allopolyploids undergo more rapid and drastic transcriptional changes due to the sudden appearance of diverged subgenomes in the same cells 6 . Genomic expression dominance has been demonstrated to be a typical feature of many allopolyploids 7 , 8 , and a large amount of data has demonstrated that genomic expression dominance is associated with asymmetric epigenetic features, such as DNA methylation 8 , 9 , histone modification 8 and chromatin compactness 10 .…”

Nanopore long-read RNAseq reveals transcriptional variations in citrus species

“…Alternative splicing (AS) is a ubiquitous process to generate different transcripts from the same gene, which modulates the diversity of mRNA and gene expression ( Laloum et al., 2018 ; Li et al., 2022 ). Four major types of AS can be classified including intron retention (IR), alternative 3’ splice site (A3), alternative 5’ splice site (A5), and exon skipping (ES) ( Hu et al., 2022 ).…”