Comparative Analysis of Alternative Splicing in Moso Bamboo and Its Dwarf Mutant, Phyllostachys edulis ‘Tubaeformis’

Abstract

Internode length is a crucial phenotypic trait of bamboo, significantly impacting its processing and utilization. Phyllostachys edulis ‘Tubaeformis’ (Shengyin Bamboo), a variety of Moso bamboo, exhibits drastically shortened internodes, making it a valuable ornamental bamboo species. We used PacBio single-molecule long-read sequencing and second-generation sequencing to identify genome-wide alternative splicing (AS) events in Moso bamboo and its dwarf mutant, Shengyin bamboo, and compared the differences between the two. Our sequencing data unveiled 139,539 AS events, with retained introns as the most prevalent events. A large number of genes were differentially alternatively spliced (DAS) between Moso bamboo and Shengyin bamboo, and genes related to RNA splicing were most significantly enriched. The high expression of SR isoforms in the 24th internode of Moso bamboo is likely the main factor leading to its greater number of alternative splicing events. Alternative splicing affects the functional domains of partial GRF, E2F, and NAM isoforms, leading to the loss of domains in some isoforms and enabling some isoforms to acquire new functional domains, and this phenomenon is more common in Shengyin bamboo. AS modifies the functional domains of certain GRF isoforms, frequently resulting in domain losses or endowing isoforms with novel domains, and this phenomenon is more common in Shengyin bamboo. We used PacBio single-molecule long-read sequencing and second-generation sequencing to identify genome-wide alternative splicing (AS) events in Moso bamboo and its dwarf mutant, Shengyin Bamboo and compared the differences between the two.