Differential Alternative Splicing Genes and Isoform Regulation Networks of Rapeseed (Brassica napus L.) Infected with Sclerotinia sclerotiorum

Abstract

Alternative splicing (AS) is a post-transcriptional level of gene expression regulation that increases transcriptome and proteome diversity. How the AS landscape of rapeseed (Brassica napus L.) changes in response to the fungal pathogen Sclerotinia sclerotiorum is unknown. Here, we analyzed 18 RNA-seq libraries of mock-inoculated and S. sclerotiorum-inoculated susceptible and tolerant B. napus plants. We found that infection increased AS, with intron retention being the main AS event. To determine the key genes functioning in the AS response, we performed a differential AS (DAS) analysis. We identified 79 DAS genes, including those encoding splicing factors, defense response proteins, crucial transcription factors and enzymes. We generated coexpression networks based on the splicing isoforms, rather than the genes, to explore the genes’ diverse functions. Using this weighted gene coexpression network analysis alongside a gene ontology enrichment analysis, we identified 11 modules putatively involved in the pathogen defense response. Within these regulatory modules, six DAS genes (ascorbate peroxidase 1, ser/arg-rich protein 34a, unknown function 1138, nitrilase 2, v-atpase f, and amino acid transporter 1) were considered to encode key isoforms involved in the defense response. This study provides insight into the post-transcriptional response of B. napus to S. sclerotiorum infection.

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

“…These results suggested that AS can work together with expression regulation to contribute to abiotic stress responses. Nevertheless, some studies indicated that AS might function independently to gene expression under abiotic and biotic stresses ( Gu et al., 2019 ; Ma et al., 2019 ; Ma et al., 2020 ; Li et al., 2022a ). Thereafter, the exact relationship between AS and expression level in response to stress needs to be further investigated in detail.…”

“…A few SR genes were certificated to exhibit responsive AS patterns under heat, drought, and salt stress conditions in wheat ( Liu et al., 2018 ). In B. napus , the AS modes of SR splicing factors have also been reported to change under different stress conditions, such as boron deficiency, S. sclerotiorum , and L. maculans ( Gu et al., 2019 ; Ma et al., 2019 ; Ma et al., 2020 ). In this study, two SR34a ( MSTRG.46899 and MSTRG.27677 ) produced different isoforms in response to dehydration and cold stresses, suggesting that there was a certain responsive relationship between dehydration and cold.…”

“…In the past, the AS events of most genes in response to stresses were identified by wet-lab experiments, while recent studies have developed the methodology for genome-wide identification of AS events and AS networks by transcriptomics, so that more splicing variations can be detected. For example, the AS landscapes ascribable to individual stress such as Sclerotinia sclerotiorum , Leptosphaeria maculans , and boron deficiency in B. napus have been illustrated ( Gu et al., 2019 ; Ma et al., 2019 ; Ma et al., 2020 ). The AS dynamics of Arabidopsis , maize, and wheat, caused by salt, drought, and cold and heat stresses, alone or in combination, were also elaborated in detail ( Ding et al., 2014 ; Thatcher et al., 2016 ; Liu et al., 2018 ).…”

Phylogenetic analysis and stress response of the plant U2 small nuclear ribonucleoprotein B″ gene family

“…The biological clock of Arabidopsis not only controls gene transcription but also influences its post-transcriptional regulation by influencing AS [ 42 ]. Six differential AS events occurred in the defence response of germs in mock-inoculated and S. sclerotiorum -inoculated susceptible and tolerant B. napus plants, as determined by an analysis of 18 RNA-seq libraries [ 43 ]. However, the potential mechanism via which splice proteins affect splicing regulation remains unclear.…”

Acorde: unraveling functionally-interpretable networks of isoform co-usage from single cell data

“…However, the extent to which AS regulation creates co-expression patterns among alternative isoforms from different genes has not yet been fully addressed. Specifically, previous studies tackling this type of isoform co-expression have either focused on specific event types, such as alternative 3' exons 84 , or solely on the identification of functionally-relevant alternative isoforms in different biological contexts 85,86 .…”