Deciphering alternative splicing patterns in multiple tissues of Ginkgo biloba important secondary metabolites

Alternative splicing (AS) is an important genetic regulation mechanism for enhancing the diversity and complexity of the transcriptome and proteome from a limited number of genes. G. biloba is a typical relict tree species with rich medicinal value; the alternative splicing characteristics of the G. biloba genome are intriguing due to its very large proportion of large introns. In this study, the genome-wide landscape of the ginkgo AS pattern was revealed through a comprehensive analysis of multiple tissues across different developmental stages. Intron retention was the dominant AS type in all tissues together with a much lower frequency compared to other plants, and the functional enrichment of different AS type-related genes also showed great differences. In addition, the AS patterns of important secondary metabolites in G. biloba, including flavonoids and terpenoids, were thoroughly analyzed. These results could be beneficial for studies on gene regulation and the synthesis mechanisms of important secondary metabolites in woody plants. •Providing a complete landscape of Ginkgo biloba alternative splicing patterns.•Revealing the relationship between alternative splicing and expression in Ginkgo biloba important metabolites.•Identifying AS-related genes involved in secondary metabolites synthesis.