Genome-Wide Alternative Splicing Patterns Modulated During Grass:Virus Interactions

Alternative splicing (AS) influences plant growth, development and response to stress. We analyzed genome-wide AS changes in Brachypodium distachyon, infected with Panicum mosaic virus (PMV) using RNA-sequencing approach. Approximately 42% of multi-exonic genes in Brachypodium are alternatively-spliced. Among the major AS types, intron-retentions predominated, followed by alternate acceptor, alternative donor and exon-skipping. We identified AS events in ~100 immune-related genes encoding receptor-like kinases, NB-LRR resistance proteins, transcription factors, RNA-silencing and splicing-associated proteins. Cloning and molecular characterization of Bd-SCL33, a serine/arginine-rich (SR) splicing factor, uncovered multiple novel intron-retaining splice-variants that are developmentally regulated and modulated during virus infection. Strikingly, Bd-SCL33 splicing patterns are conserved during infections of additional grass-infecting viruses including Brome mosaic virus, Barley stripe mosaic virus, Maize mild mottle virus, Sorghum yellow banding virus, Wheat streak mosaic virus and Foxtail mosaic virus. Together, these analyses provide new insights into virus-triggered AS landscapes in plants.