Differential Intron Retention Is a Key Component of Alternative Splicing-Driven Adaptation to Abiotic Stress in Transcriptome of Western Poplar (Populus trichcarpa)

Alternative splicing (AS) of precursor messenger RNAs (pre-mRNAs) is a widespread phenomenon in plants, with 42-61% of intron-containing genes exhibiting AS. Intron retention (IR) is a predominant class of AS events in plants. We investigated the repertoire and extent of the IR in key tissue types of western poplar under osmotic (dehydration or high salinity) and thermal stresses (heat or cold). Stress-induced differential IR (DiffIR) events were identified using the iDiffIR software. Abiotic stresses induced wide spectrum of DiffIR across poplar transcriptome. A total of 1654 unique genes in leaf, root, and xylem tissues harbored DiffIR events induced by both short- and long-term cold, dehydration, high salinity, and heat treatments. Osmotic stress produced two subsets of differentially retained introns: a) DiffIR events regulated exclusively by a drought and/or high salinity and b) ubiquitous DiffIR events which were also induced by other abiotic treatments. Only limited proportions of DiffIR events overlapped between short- and long-term dehydration treatments. However, some transcripts harboring multiple DiffIR events displayed a “super- stress response” across a broad spectrum of treatments. Stress-driven DiffIR were present in many key gene families regulating cell wall metabolism, splicing, stress-response, plant development, and circadian rhythms.