Comprehensive discovery of salt-responsive alternative splicing events based on Iso-Seq and RNA-seq in grapevine roots

• Published in: Environmental and experimental botany 2021-12, Vol.192, p.104645, Article 104645
• Main Authors: Jin, Zhongxin, Lv, Xinning, Sun, Yushuai, Fan, Zongbao, Xiang, Guangqing, Yao, Yuxin
• Format: Article
• Language: English
• Subjects: Alternative polyadenylation; Alternative splicing; Grapevine; Isoform sequencing (Iso-Seq); RNA-seq; Salt stress
• ISSN: 0098-8472; 1873-7307
• DOI: 10.1016/j.envexpbot.2021.104645

•Improving the annotation file to identify more alternative splicing (AS) events.•A total of 1,466 AS events responded to salt stress in grapevine roots.•Salt-responsive AS events affect protein products and miRNA binding.•Salt-induced spliceosomal proteins were identified.•An innovative pipeline to discover the interactions between AS and alternative polyadenylation. Alternative splicing (AS) can enhance the adaptive capacity of organisms to respond to abiotic stresses via transcriptome plasticity; however, the mechanism underlying the responses of AS events to salt remains unclear in grapevine roots. In this study, an optimized genome annotation file was generated using Iso-Seq and RNA-seq data of grapevine roots. Based on the updated file, a total of 8,453 AS events across five types were identified in A17 grapevine roots, of which retained intron (RI) was the most dominant type. A total of 1,466 AS events affiliated with 1,113 genes responded to salt stress in grapevine roots. A global decrease in the proportion of inclusion isoforms was demonstrated, indicating that salt stress promoted the production of shorter isoforms. Only 206 salt-responsive AS events were affiliated with differentially expressed genes, indicating little overlap between transcriptional regulation and post-transcriptional regulation. A total of 672 and 410 AS events affected the length of protein products and miRNA binding, respectively. Differentially spliced genes were primarily related to RNA processing, nucleic acid binding, and ion channel activity. In addition, the salt-induced spliceosomal protein genes LSM2 and SRSF1 were identified, and their possible roles in regulating AS events were inferred. Moreover, we drafted an approach to explore possible interactions between AS and alternative polyadenylation (APA) using Iso-Seq data. Overall, these findings provide a comprehensive understanding of salt-responsive AS events in grapevine roots, providing insight into the molecular mechanism of salt tolerance in grapevine.