title: A deep survey of alternative splicing in grape reveals changes in the splicing machinery related to tissue, stress condition and genotype.
abstract: BACKGROUND
  Alternative splicing (AS) significantly enhances transcriptome complexity. It is differentially regulated in a wide variety of cell types and plays a role in several cellular processes. Here we describe a detailed survey of alternative splicing in grape based on 124 SOLiD RNAseq analyses from different tissues, stress conditions and genotypes.
  
  
  RESULTS
  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. Several gene structures have been improved and alternative splicing was described for about 30% of the genes. A link between AS and miRNAs was shown in 139 genes where we found that AS affects the miRNA target site. 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.
  
  
  CONCLUSIONS
  As described in Arabidopsis, also grape displays a marked AS tissue-specificity, while stress conditions produce splicing changes to a minor extent. Surprisingly, some distinctive splicing features were also observed between genotypes. 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. 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.
authors.forename: Nicola
authors.initials: N
authors.lastname: Vitulo
authors.forename: Claudio
authors.initials: C
authors.lastname: Forcato
authors.forename: Elisa Corteggiani
authors.initials: EC
authors.lastname: Carpinelli
authors.forename: Andrea
authors.initials: A
authors.lastname: Telatin
authors.forename: Davide
authors.initials: D
authors.lastname: Campagna
authors.forename: Michela
authors.initials: M
authors.lastname: D'Angelo
authors.forename: Rosanna
authors.initials: R
authors.lastname: Zimbello
authors.forename: Massimiliano
authors.initials: M
authors.lastname: Corso
authors.forename: Alessandro
authors.initials: A
authors.lastname: Vannozzi
authors.forename: Claudio
authors.initials: C
authors.lastname: Bonghi
authors.forename: Margherita
authors.initials: M
authors.lastname: Lucchin
authors.affiliation: CRIBI Biotechnology Centre, University of Padua, Padua, Italy. giorgio.valle@unipd.it.
authors.forename: Giorgio
authors.initials: G
authors.lastname: Valle
mesh_terms: D000222:Adaptation, Physiological / Q000235:genetics; D017398:Alternative Splicing / Q000235:genetics*; D029681:Arabidopsis Proteins / Q000235:genetics / Q000378:metabolism; D030541:Databases, Genetic; D030561:Databases, Nucleic Acid; D019143:Evolution, Molecular; D018506:Gene Expression Regulation, Plant; D017343:Genes, Plant; D005838:Genotype; D035683:MicroRNAs / Q000235:genetics / Q000378:metabolism; D009928:Organ Specificity / Q000235:genetics*; D025341:Principal Component Analysis; D020033:Protein Isoforms / Q000235:genetics / Q000378:metabolism; D022661:RNA, Untranslated / Q000235:genetics / Q000378:metabolism; D013312:Stress, Physiological / Q000235:genetics*; D027843:Vitis / Q000235:genetics*
chemical_list: D029681:Arabidopsis Proteins; D035683:MicroRNAs; D020033:Protein Isoforms; D022661:RNA, Untranslated
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