Transcriptome-wide alternative splicing modulation during Coffea-Hemileia vastatrix interaction

During plant-pathogen interaction, Alternative Splicing (AS) can significantly impact resistance or susceptibility, modify the protein expression profile or modulating the transcription of resistance-associated genes. Studying AS events in coffee plants interacting with Hemileia vastatrix can bring new perspectives to the understanding of this pathosystem. In this way, we carried out the first study of AS in coffee plants in the compatible (Caturra CIFC 19/1–H. vastatrix) and incompatible (HdT CIFC 832/1–H. vastatrix) interactions. RNAseq data from CIFC 19/1 and CIFC 832/1 during infection with urediniospores of H. vastatrix at 12, 24 and 96 hours after inoculation (hai) were used. First, a general profile of splicing events associated with genes and biological processes relevant to the plant-pathogen interaction was drawn. Then, the validation and quantification of AS events that impact the structure of protein domains were analyzed. Genes with validated AS events suggest that Exon Skipping (ES) and Intron retention (IR) events in genes LOC113701067 (Transcription factor basic Helix-Loop-Helix –bHLH) and LOC113711504 (leucine-rich repeat), respectively, may affect processes involved with the control of pathogen entry via the stomata, among other essential processes involved in the defense response. Also, even after 0 hours of inoculation, plants resistant to CIFC 832/1 showed a higher expression level of the validated events. These data are until now unpublished with no reports in the literature of splicing studies with alternative directions for the coffee-H stattrix pathosystem.