Transcriptome-wide characterization of alternative splicing in five drug-type cultivars of Cannabis sativa

Cannabis sativa is widely used for fiber, medicinal, and other purposes, and many cultivars exist, yielding varying proportions of cannabinoids and terpenes. There is considerable interest in characterizing genomes and transcriptomes of C. sativa. Alternative splicing (AS) is a fundamental aspect of gene expression that results in multiple types of mRNAs produced by differential splicing. Transcriptome-wide identification of AS events in drug-type cultivars of C. sativa has not been reported. Here we identified AS events using a transcriptome dataset derived from five drug-type cultivars with divergent chemotypes. Intron retention is the most common event type, followed by alternative acceptor, alternative donor, and skipped exons. We also sought to assess conservation of AS events among cultivars. We found 547 events (5%) unique to a single cultivar, 2661 (25%) shared by 2-4 cultivars, and 7569 (70%) common to all five cultivars. Genes with AS events in each set were analyzed for gene ontology enrichment, showing that genes with AS unique to a single cultivar are enriched for molecular functions related to interactions with ATP, and processes involving transport within cells and across membranes. These results provide insights into the conservation and variation of AS events in multiple cultivars of C. sativa.