A deep survey of alternative splicing in grape reveals changes in the splicing machinery related to tissue, stress condition and genotype
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  • 作者：Nicola Vitulo (1)
    Claudio Forcato (1)
    Elisa Corteggiani Carpinelli (1)
    Andrea Telatin (1)
    Davide Campagna (4)
    Michela D鈥橝ngelo (1)
    Rosanna Zimbello (1)
    Massimiliano Corso (2)
    Alessandro Vannozzi (2)
    Claudio Bonghi (2)
    Margherita Lucchin (2) (3)
    Giorgio Valle (1) (4)

    1. CRIBI Biotechnology Centre     ; University of Padua ; Padua ; Italy
    4. Department of Biology     ; University of Padua ; Padua ; Italy
    2. Department of Agronomy     ; Food ; Natural resources ; Animals and Environment ; DAFNAE ; University of Padua ; Padua ; Italy
    3. CIRVE     ; Centre for Research in Viticulture and Enology ; University of Padua ; Padua ; Italy
  • 关键词：Alternative splicing ; Transcriptome ; RNAseq ; Grapevine
  • 刊名：BMC Plant Biology
  • 出版年：2014
  • 出版时间：December 2014
  • 年：2014
  • 卷：14
  • 期：1
  • 全文大小：952 KB
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  • 刊物主题：Plant Sciences; Agriculture; Tree Biology;
  • 出版者：BioMed Central
  • ISSN：1471-2229
文摘
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.

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