Exploration of alternative splicing events in 10 different grapevine cultivars

The complex dynamics that regulate the extent and shape of a plant transcriptome are a fascinating but not fully elucidated topic. Among phenomena involved, alternative splicing (AS) is one of the lesser understood ones. For many years AS was underestimated in plants but since the introduction of NGS techniques the number of plant genes estimated to be alternative spliced has exponentially increased. Here, we have performed high-throughput transcript sequencing of 10 grapevine cultivars which resulted in the first high coverage atlas for the grape berry transcriptome. We also developed findAS a custom software for AS prediction proposing a new detection approach. We demonstrate that at least 40% of multi-exonic genes undergo AS and a large class of low abundance alternative events is present within the ~110,000 currently annotated splice junctions. Our analysis shows than 70% of all events has a relative low expression and alternative splice sites seems to be enriched near the constitutive ones, remarkably alternative events are extensively conserved among 10 cultivars. While events frequency and positions seem to indicate a major role of “stochastic noise” in splice site selection, the high level of conservation seems point toward a functional role