Exploration of alternative splicing events in ten different grapevine cultivars

BMC Genomics

Research Article

Milvia Luisa Racchi¹  Silvio C. E. Tosatto²  Lieven Sterck³  Yves Van de Peer⁴  Alessandro Cestaro⁵  Riccardo Velasco⁵  Emanuela Coller⁵  Elisa Asquini⁵  Emilio Potenza⁶ 

[1] Department of Agri-Food Production and Environmental Sciences, Università degli Studi di Firenze, 50121, Firenze, Italy;Department of Biomedical Sciences, Università degli Studi di Padova, 35131, Padova, Italy;Department of Plant Systems Biology, VIB, Ghent, Belgium;Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium;Department of Plant Systems Biology, VIB, Ghent, Belgium;Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium;Department of Genetics, Genomics Research Institute, University of Pretoria, Pretoria, South Africa;Fondazione Edmund Mach, Via E. Mach 1, 38010 S., Michele all’Adige, TN, Italy;Fondazione Edmund Mach, Via E. Mach 1, 38010 S., Michele all’Adige, TN, Italy;Department of Agri-Food Production and Environmental Sciences, Università degli Studi di Firenze, 50121, Firenze, Italy;Department of Plant Systems Biology, VIB, Ghent, Belgium;Department of Biomedical Sciences, Università degli Studi di Padova, 35131, Padova, Italy;

关键词: Alternative splicing;    Vitis vinifera;    RNA-seq;    Stochastic noise;   

DOI  :  10.1186/s12864-015-1922-5

 received in 2014-05-22, accepted in 2015-09-11,  发布年份 2015

来源: Springer

【 摘 要 】

BackgroundThe 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.ResultsHere, 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.ConclusionsOur 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.

【 授权许可】

CC BY   
© Potenza et al. 2015