Transcriptome-wide alternative splicing modulation during plant-pathogen interactions in wheat.

Alternative splicing (AS) enhances the diversities of both transcripts and proteins in eukaryotes, which contribute to stress adaptation. To catalog wheat (Triticum aestivum L.) AS genes, we characterized 45 RNA-seq libraries from wheat seedlings infected by powdery mildew, Blumeria graminis f. sp. tritici (Bgt) or stripe rust fungus, Puccinia striiformis f. sp. tritici (Pst). We discovered that 11.2% and 10.4% of the multiexon genes had AS transcripts during Bgt and Pst infections, respectively. In response to fungal infection, wheat modulated AS not only in disease resistance proteins, but also in splicing related factors. Apart from the stress induced or activated splicing variants by pathogen, the differential expression profiles were fold increased through changing the ratio of full spliced transcripts versus intron retention (IR) transcripts. Comparing AS transcripts produced by the same gene in Bgt with Pst stress, the spliced terminal exons and the stranded introns are independent and different. This demonstrated that differential induction of specific splice variants were activated against two fungal pathogens. The specific induced AS genes in the Pst-resistant plants were enriched in improving the membrane permeability and protein modification ability, whereas gene expression involved in protein translation and transport were strengthened in Pst-susceptible plants.