Alternative Splicing Identification and Analysis of Its Regulation in Coptis chinensis Franch. Under Environmental Adaptation and Biosynthesis

Coptis chinensis Franch., a traditional Chinese medicine (TCM), exhibits pharmacological effects including antipyretic and analgesic, anti-arrhythmic and anti-tumor. Alternative splicing (AS) significantly impacts plant growth, development, and biosynthesis, yet its role in C. chinensis remains poorly understood. This study used transcriptome sequencing to analyze and identify AS events in this species. Functional annotation and enrichment analysis of these AS genes were conducted. Moreover, we screened the key environmental variables that affect the growth of C. chinensis using the Biomod2 model and designed stress experiments to further validate AS events and their regulatory effects on this plant. Two types of AS events were identified: skipped exon (SE) and mutually exclusive exons (MXE), with SE-type being predominant. These AS genes were enriched in 189 Gene Ontology and 59 Kyoto Encyclopedia of Genes and Genomes entries. These included entries related to environmental adaptations, such as "response to heat," "protein phosphorylation," "starch and sucrose metabolism," and five entries related to benzylisoquinoline alkaloid biosynthesis. Biomod2 model results showed that Temperature Seasonality (Bio4) was the environmental variable with the highest contribution (45.58%). Additional validation experiments revealed that the splicing index value of the AS genes in C. chinensis exhibited an initial increase followed by a decrease with the extension of the heat stress time, while gene expression also generally increased. This study highlights the crucial role of AS in the environmental adaptation and benzylisoquinoline alkaloid biosynthesis of C. chinensis, providing a theoretical basis for the cultivation and improvement of the varieties of this TCM.