Specificity Analysis of Alternative Splicing During Botrytis cinerea Infection of Different Hosts

Alternative splicing (AS) is a significant post-transcriptional regulatory mechanism that facilitates environmental adaptation in fungi. However, the conservation of this mechanism and its host specificity during the infection of various hosts by B. cinerea remain ambiguous. This study utilized strand-specific RNA sequencing to perform a comparative analysis of genome-wide AS patterns during the infection of tomato and strawberry by B. cinerea. A comparative analysis identified a total of 1714 AS events and 1130 associated genes across the two hosts, alongside a significant number of host-specific events. Common alternatively spliced genes were predominantly enriched in processes related to gene expression regulation and signal transduction, whereas host-specific genes displayed distinct functional enrichment characteristics and temporal dynamics in their Percent Spliced In (PSI) patterns. Notably, introns linked to AS were generally longer than those associated with constitutive splicing and predominantly featured canonical GT-AG splice boundaries. Furthermore, the magnitude of PSI changes in host-specific events was greater than that observed in common events. This study reveals that B. cinerea exhibits both conserved and host-dependent AS regulatory programs, providing new insights into its post-transcriptional regulatory plasticity during the infection of various plant hosts.