Integrative analysis of transcriptome and alternative splicing uncovers the regulatory network of Alternaria alternata resistance in sweet cherry

• Following A. alternata infection, the expression of desA3, FAD2, ACOT1_2_4 , and LOX5 genes was significantly upregulated in sweet cherry cultivar Q8, but not in Q9. • A. alternata infection altered alternative splicing of LOX5 gene. • Intron retention of LOX5 increased significantly in cultivar Q9, but not in cultivar Q8, following A. alternata infection. Transcription and post-transcriptional regulation of RNA in plants play a pivotal role in their interactions with microorganisms. In particular, changes in transcription and alternative splicing (AS) of immune genes are involved in the disease resistance process in plants. The objective of this study was to mine immune-related genes in sweet cherry and investigate their mechanism of resistance to Alternaria alternata at the transcriptional and AS levels. Here, by employing RNA sequencing and AS analysis, we identified distinct patterns in the expression of immune pathway-related genes and AS of LOX5 gene in resistant and susceptible sweet cherry genotypes upon pathogen infection. Our results show that A. alternata infection induces global transcriptomic changes in the leaves of the resistant cultivar Q8 and the susceptible cultivar Q9 of sweet cherry. Notably, key genes involved in unsaturated fatty acid biosynthesis ( desA3, FAD2, ACOT1_2_4 ) and critical genes in linoleic acid metabolism ( LOX5 ) were upregulated in cultivar Q8 at 3 and 9 days post-inoculation (dpi), whereas only a subset of these genes exhibited slight upregulation in cultivar Q9 at the same time points. Additionally, retention of the first intron of LOX5 gene was markedly ( P < 0.05) increased in the susceptible cultivar Q9 at 3 and 9 dpi, whereas such retention showed no significant increase in the resistant cultivar Q8 and even decreased significantly ( P < 0.05) at 9 dpi. Our results suggest that sweet cherry may confer disease resistance by modulating both the expression level and AS of LOX5 gene. This study advances our understanding of the interaction between sweet cherry and A. alternata , and reveals that modulation of expression levels and AS of immune-related genes in sweet cherry constitutes a critical adaptive strategy in the dynamic interaction between the host and pathogenic microbes.