title: Exploration of alternative splicing events in ten different grapevine cultivars.
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.
authors.affiliation: Fondazione Edmund Mach, Via E. Mach 1, 38010 S., Michele all'Adige, TN, Italy. emilio.potenza@bio.unipd.it.|Department of Agri-Food Production and Environmental Sciences, Università degli Studi di Firenze, Firenze, 50121, Italy. emilio.potenza@bio.unipd.it.|Department of Plant Systems Biology, VIB, Ghent, Belgium. emilio.potenza@bio.unipd.it.|Department of Biomedical Sciences, Università degli Studi di Padova, Padova, 35131, Italy. emilio.potenza@bio.unipd.it.
authors.forename: Emilio
authors.initials: E
authors.lastname: Potenza
authors.affiliation: Department of Agri-Food Production and Environmental Sciences, Università degli Studi di Firenze, Firenze, 50121, Italy. milvia.racchi@unifi.it.
authors.forename: Milvia Luisa
authors.initials: ML
authors.lastname: Racchi
authors.affiliation: Department of Plant Systems Biology, VIB, Ghent, Belgium. liste@psb.vib-ugent.be.|Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium. liste@psb.vib-ugent.be.
authors.forename: Lieven
authors.initials: L
authors.lastname: Sterck
authors.affiliation: Fondazione Edmund Mach, Via E. Mach 1, 38010 S., Michele all'Adige, TN, Italy. emanuela.coller@fmach.it.
authors.forename: Emanuela
authors.initials: E
authors.lastname: Coller
authors.affiliation: Fondazione Edmund Mach, Via E. Mach 1, 38010 S., Michele all'Adige, TN, Italy. elisa.asquini@fmach.it.
authors.forename: Elisa
authors.initials: E
authors.lastname: Asquini
authors.affiliation: Department of Biomedical Sciences, Università degli Studi di Padova, Padova, 35131, Italy. silvio.tosatto@unipd.it.
authors.forename: Silvio C E
authors.initials: SC
authors.lastname: Tosatto
authors.affiliation: Fondazione Edmund Mach, Via E. Mach 1, 38010 S., Michele all'Adige, TN, Italy. riccardo.velasco@fmach.it.
authors.forename: Riccardo
authors.initials: R
authors.lastname: Velasco
authors.affiliation: Department of Plant Systems Biology, VIB, Ghent, Belgium. yves.vandepeer@psb.vib-ugent.be.|Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium. yves.vandepeer@psb.vib-ugent.be.|Department of Genetics, Genomics Research Institute, University of Pretoria, Pretoria, South Africa. yves.vandepeer@psb.vib-ugent.be.
authors.forename: Yves
authors.initials: Y
authors.lastname: Van de Peer
authors.affiliation: Fondazione Edmund Mach, Via E. Mach 1, 38010 S., Michele all'Adige, TN, Italy. alessandro.cestaro@fmach.it.
authors.forename: Alessandro
authors.initials: A
authors.lastname: Cestaro
mesh_terms: D017398:Alternative Splicing / Q000235:genetics*; D059014:High-Throughput Nucleotide Sequencing; D012326:RNA Splicing / Q000235:genetics; D027843:Vitis / Q000235:genetics*