ArticleBMC plant biology2014
A deep survey of alternative splicing in grape reveals changes in the splicing machinery related to tissue, stress condition and genotype.
Article in BMC plant biology, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 141 papers, 2 of them syntheses that pooled it.
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Who cites it
141 citing papers in PubMed, 2 syntheses or guidelines pooled it.
- Network aggregation improves gene function prediction of grapevine gene co-expression networks.Plant molecular biology · 2020Pooled it
- Comprehensive Workflow for the Genome-wide Identification and Expression Meta-analysis of the ATL E3 Ubiquitin Ligase Gene Family in Grapevine.Journal of visualized experiments : JoVE · 2017Pooled it
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- Integrating Dense Genotyping with High-Throughput Phenotyping Empowers the Genetic Dissection of Berry Quality and Resilience Traits in Grapevine.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- Grape ripening speed slowed down using natural variation.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2025Article
- Differences in alternative splicing and their potential underlying factors between animals and plants.Journal of advanced research · 2024Review
- Biography ofHorticulture research · 2024Article
- Gene expression and alternative splicing contribute to adaptive divergence of ecotypes.Heredity · 2024Article
- Responsive Alternative Splicing Events ofInternational journal of molecular sciences · 2024Article
- RNA-seq analysis reveals transcriptome reprogramming and alternative splicing during early response to salt stress in tomato root.Frontiers in plant science · 2024Article
- The grapevine ABC transporter B family member 15 is aFrontiers in plant science · 2024Article
- An improved reference of the grapevine genome reasserts the origin of the PN40024 highly homozygous genotype.G3 (Bethesda, Md.) · 2023Article
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- The Combination of Both Heat and Water Stresses May Worsen Botryosphaeria Dieback Symptoms in Grapevine.Plants (Basel, Switzerland) · 2023Article
- Boosting grapevine breeding for climate-smart viticulture: from genetic resources to predictive genomics.Frontiers in plant science · 2023Review
- Grape Berry Responses to Sequential Flooding and Heatwave Events: A Physiological, Transcriptional, and Metabolic Overview.Plants (Basel, Switzerland) · 2022Article
- The grapevine aspartic protease gene family: characterization and expression modulation in response to Plasmopara viticola.Journal of plant research · 2022Article
81 more citing papers are in PubMed but not listed here.
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Authors and funding
12 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundAlternative 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.
resultsWe 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.
conclusionsAs 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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