Abstract:
BACKGROUND : The complex dynamics of gene regulation in plants are still far from being fully understood. Among
many factors involved, alternative splicing (AS) in particular is one of the least well documented. For many years, AS
has been considered of less relevant in plants, especially when compared to animals, however, since the introduction
of next generation sequencing techniques the number of plant genes believed to be alternatively spliced has
increased exponentially.
RESULTS : Here, we performed a comprehensive high-throughput transcript sequencing of ten different grapevine
cultivars, which resulted in the first high coverage atlas of the grape berry transcriptome. We also developed findAS, a
software tool for the analysis of alternatively spliced junctions. We demonstrate that at least 44 % of multi-exonic genes
undergo AS and a large number of low abundance splice variants is present within the 131.622 splice junctions we
have annotated from Pinot noir.
CONCLUSIONS : Our analysis shows that ~70 % of AS events have relatively low expression levels, furthermore alternative
splice sites seem to be enriched near the constitutive ones in some extent showing the noise of the splicing
mechanisms. However, AS seems to be extensively conserved among the 10 cultivars.
