Dissecting alternative splicing patterns of the Rheum palmatum complex with different contents of medicinal constituents

Rhubarb (Da Huang) is an important traditional Chinese herbal medicine. The content of medicinal constituents is a key determinant of its quality. Enhancing levels of these medicinal ingredients through genetic improvement is a powerful approach to bridge the gap between surging market demand and dwindling resources, yet this strategy is currently impeded by an incomplete comprehension of the mechanism of metabolite differences in rhubarb, especially at a post-transcriptional level. In this study, we investigated the alternative splicing (AS) landscapes of two Rheum materials ─ QHZK and SNPL ─ which exhibit contrasting levels of anthraquinones. Different types of AS events were detected in the roots, stems, leaves, and flowers of these two Rheum materials, with alternative 3’ splice sites (A3SS) and intron retention (IR) being the most predominant AS types. A total of 2,070 genes were identified as undergoing differential alternative splicing (DAS) in different tissues between the two Rheum materials. Weighted isoform-based co-expression network analysis pinpointed multiple hub DAS candidate genes with potential roles in mRNA processing, transcription regulation, splicing, and metabolite synthesis. This study unveils novel perspectives on the potential impact of post-transcriptional regulation on the difference of medicinal constituents in rhubarb. The newly identified isoforms of candidate genes not only enriches our understanding of the complex regulatory landscape in rhubarb, but also could be a valuable resource for the genetic improvement of the R. palmatum complex in the future.