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Exploration of alternative splicing events in ten different grapevine cultivars

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Bioinformatics: from nucleotids to networks (N2N)
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 similar to 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.
Keywords
MESSENGER-RNA, GENE, VITIS-VINIFERA, RNA-SEQ, STOCHASTIC NOISE, NATURAL ANTISENSE TRANSCRIPTS, Stochastic noise, RNA-seq, Vitis vinifera, Alternative splicing, ARABIDOPSIS, COMPLEXITY, QUANTIFICATION, DOMESTICATION

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Chicago
Potenza, Emilio, Milvia Luisa Racchi, Lieven Sterck, Emanuela Coller, Elisa Asquini, Silvio CE Tosatto, Riccardo Velasco, Yves Van de Peer, and Alessandro Cestaro. 2015. “Exploration of Alternative Splicing Events in Ten Different Grapevine Cultivars.” Bmc Genomics 16.
APA
Potenza, E., Racchi, M. L., Sterck, L., Coller, E., Asquini, E., Tosatto, S. C., Velasco, R., et al. (2015). Exploration of alternative splicing events in ten different grapevine cultivars. BMC GENOMICS, 16.
Vancouver
1.
Potenza E, Racchi ML, Sterck L, Coller E, Asquini E, Tosatto SC, et al. Exploration of alternative splicing events in ten different grapevine cultivars. BMC GENOMICS. 2015;16.
MLA
Potenza, Emilio, Milvia Luisa Racchi, Lieven Sterck, et al. “Exploration of Alternative Splicing Events in Ten Different Grapevine Cultivars.” BMC GENOMICS 16 (2015): n. pag. Print.
@article{6959206,
  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 similar to 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.},
  articleno    = {706},
  author       = {Potenza, Emilio and Racchi, Milvia Luisa and Sterck, Lieven and Coller, Emanuela and Asquini, Elisa and Tosatto, Silvio CE and Velasco, Riccardo and Van de Peer, Yves and Cestaro, Alessandro},
  issn         = {1471-2164},
  journal      = {BMC GENOMICS},
  keyword      = {MESSENGER-RNA,GENE,VITIS-VINIFERA,RNA-SEQ,STOCHASTIC NOISE,NATURAL ANTISENSE TRANSCRIPTS,Stochastic noise,RNA-seq,Vitis vinifera,Alternative splicing,ARABIDOPSIS,COMPLEXITY,QUANTIFICATION,DOMESTICATION},
  language     = {eng},
  pages        = {9},
  title        = {Exploration of alternative splicing events in ten different grapevine cultivars},
  url          = {http://dx.doi.org/10.1186/s12864-015-1922-5},
  volume       = {16},
  year         = {2015},
}

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