To splice or to missplice: Genome-wide alternative splicing changes occurring during plant virus infection
Kranthi K. Mandadi
Department of Plant Pathology & Microbiology, Texas A&M AgriLife Research & Extension Center, 2415 E. Highway 83, Weslaco, TX 78596
Alternative splicing is a eukaryotic post-transcriptional biological process that promotes transcriptome and proteome diversity, and influences growth, development and response to stress. For example, in humans, ~95% of genes are alternatively spliced, and aberrant alternative splicing events are linked to multiple hereditary diseases such as cause aberrant splicing underpin cystic fibrosis, muscular dystrophy, and Progeria Syndrome1. In a manner similar to animals, alternative splicing has important biological consequences for plant growth and development, flowering, circadian clock function, and stress responses2.
We have analyzed genome-wide changes in alternative splicing occurring during a plant-virus interaction3,4,5. For this, we utilized the model grass, Brachypodium distachyon, and infected it with Panicum mosaic virus (PMV) and its satellite virus (SPMV)—causal agents of St. Augustine grass decline6. High-quality total RNA was isolated from healthy and virus infected plants, and was subjected to Illumina high throughput paired-end RNA-sequencing.The resulting bioinformatics analysis revealed that about 42% of mRNAs with more than one exon were alternatively spliced in Brachypodium. Analysis of the different types of alternative splicing events showed that ~36% involved intron retention, ~41% involved alternate donor or acceptor sites, and ~ 9% involved exon skipping, while ~14% were found to be complex, consisting of duplicated or combinations of the aforementioned types. The low frequency of exon skipping events, a characteristic of plant alternative splicing, is in striking contrast to those occurring in animal systems, where exon skipping is predominant.
Furthermore, we found that virus infections increased the overall number of alternative splicing events in Brachypodium, without affecting the overall ratio of different types of alternative splicing events. Among the spliced genes, we identified ~600 genes that showed changes in splicing pattern in response to virus infection. These included ~100 immune-related genes encoding receptor-like kinases, NB-LRR resistance proteins, transcription factors, RNA-silencing and splicing-associated proteins. Further investigations of these alternative spliced events, and of their encoded proteins, should inform the underlying mechanisms of alternative splicing processes related to plant immune-signaling.
Mandadi KK, & Scholthof KB (2015). Genome-wide analysis of alternative splicing landscapes modulated during plant-virus interactions in Brachypodium distachyon. The Plant cell, 27 (1), 71-85 PMID: 25634987
1. Staiger D, & Brown JW (2013). Alternative splicing at the intersection of biological timing, development, and stress responses. The Plant cell, 25 (10), 3640-56 PMID: 24179132
2. Reddy AS, Marquez Y, Kalyna M, & Barta A (2013). Complexity of the alternative splicing landscape in plants. The Plant cell, 25 (10), 3657-83 PMID: 24179125
3. Mandadi KK, & Scholthof KB (2015). Genome-wide analysis of alternative splicing landscapes modulated during plant-virus interactions in Brachypodium distachyon. The Plant cell, 27 (1), 71-85 PMID: 25634987
4. Mandadi KK, & Scholthof KB (2015). Genomic architecture and functional relationships of intronless, constitutively- and alternatively-spliced genes in Brachypodium distachyon. Plant signaling & behavior, 10 (8) PMID: 26156297
5. Mandadi KK, Pyle JD, & Scholthof KB (2015). Characterization of SCL33 splicing patterns during diverse virus infections in Brachypodium distachyon. Plant signaling & behavior, 10 (8) PMID: 26179847
6. Cabrera, O., & Scholthof, K. (1999). The Complex Viral Etiology of St. Augustine Decline Plant Disease, 83 (10), 902-904 DOI: 10.1094/PDIS.19126.96.36.1992