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Recently, deep sequencing of the transcriptome using high-throughput RNA sequencing (RNAseq) increased this estimate showing that more that 60% of intron-containing genes in Arabidopsis are alternatively spliced. For example, 20–30% of transcripts were found to be alternatively spliced in both Arabidopsis thaliana and rice ( Oryza sativa) by employing large-scale EST-genome alignments. Different studies based on computational analysis on both expressed sequence tags and high-throughput RNA sequencing provide an estimate of the frequency of these events. Īlternative splicing (AS) is one of the main mechanisms that forge transcriptome plasticity and proteome diversity. Recent works pointed out the extensive diffusion of these phenomena in plants and their importance in gene expression and stress response. However the eukaryotic transcriptome, and in particular the plant transcriptome, is far more complex than previously believed, alternative splicing and non coding transcripts being amongst the major causes contributing to this complexity. The availability of the genomic sequence gave the opportunity to conduct several genome-wide studies focused on different aspects of grape biology such as berry development and response to different biotic and abiotic stresses. The complete genome sequence was obtained in 2007 by two independent projects. Several reasons make grapevine particularly interesting: it is the most cultivated fruit plant covering approximately 7.5 million hectares in 2012 ( ), with a long history of domestication, as well as a useful model organism since it seems to have maintained the ancestral genomic structure of the primordial flowering plants. The finding that a part the splicing machinery can change in closely related organisms can lead to some interesting hypotheses for evolutionary adaptation, that could be particularly relevant in the response to sudden and strong selective pressures. This was further supported by the observation that the panel of Serine/Arginine-rich splicing factors show a few, but very marked differences between genotypes. Surprisingly, some distinctive splicing features were also observed between genotypes. ConclusionsĪs described in Arabidopsis, also grape displays a marked AS tissue-specificity, while stress conditions produce splicing changes to a minor extent. A quantitative analysis of the isoforms indicated that most of the spliced genes have one major isoform and tend to simultaneously co-express a low number of isoforms, typically two, with intron retention being the most frequent alternative splicing event. A link between AS and miRNAs was shown in 139 genes where we found that AS affects the miRNA target site. Several gene structures have been improved and alternative splicing was described for about 30% of the genes.
GPASS BROWSER ALTERNATIVES UPDATE
We used the RNAseq data to update the existing grape gene prediction with 2,258 new coding genes and 3,336 putative long non-coding RNAs. Here we describe a detailed survey of alternative splicing in grape based on 124 SOLiD RNAseq analyses from different tissues, stress conditions and genotypes. It is differentially regulated in a wide variety of cell types and plays a role in several cellular processes. Alternative splicing (AS) significantly enhances transcriptome complexity.