Transcriptomic Analyses and Alternative Splicing Landscapes of Brachypodium Infected with Panicum Mosaic Virus

In plants and animals, biotic and abiotic stresses trigger genome-wide changes in gene expression. Variations in alternative splicing (AS) of genes during stress also increase the proteome diversity of the cell and influence signal transduction and adaptation. To analyze these effects during plant:virus interactions, we performed RNA-sequencing analyses of Brachypodium distachyon (Brachypodium) infected with Panicum mosaic virus (PMV). We used Tuxedo workflow for transcriptome assembly, differential gene, isoform and splicing analyses. Our analyses identified at-least 24,000 transcripts in 18,000 gene loci (~1.3 transcripts per locus) in Brachypodium that are expressed with two or more Fragments Per Kilobase of transcript per Million (FPKM) mapped fragments. About 1,800 of these gene loci are novel that mapped to previously un-annotated regions of the Brachypodium genome. While about 600 gene loci had differential splice junctions when compared to the reference Brachypodium gene annotations (Ensembl v1.0.20). Among the major types of alternative splicing events analyzed, intron-retention and alternate acceptor (3’-splice site) events appeared more predominant in Brachypodium, followed by alternative donor (5’-splice site) and exon-skipping events. PMV-infection triggered differential alternative splicing of approximately 800 genes. Gene-ontology enrichment analysis of the differential alternative spliced genes revealed over-represented functional categories in primary metabolism, transport, transcription, protein modification and signal transduction.