Grape Database

Grape Database provides integrated genomic and transcriptomic data and analyses focused on alternative splicing (AS) in grape, enabling characterization of splicing events, isoform expression, and miRNA-related regulatory interactions.

Key Features:

• Access Modes: BLAST-based sequence similarity searches and a genome browser enable exploration of gene loci and annotations.
• Alternative Splicing Insights: RNAseq analyses from 124 SOLiD experiments support updated gene predictions with 2,258 new coding genes, 3,336 putative long non-coding RNAs, improved gene structures, and annotation of AS events for approximately 30% of genes.
• miRNA Interaction: Annotation of AS events that affect miRNA target sites in 139 genes documents links between splicing and post-transcriptional regulation.
• Quantitative Isoform Analysis: Isoform expression quantification shows most spliced genes have a predominant major isoform with a limited number of co-expressed isoforms and identifies intron retention as the most frequent AS event.
• Tissue-Specific and Stress-Induced Splicing Patterns: Documented marked tissue-specificity of AS in grape and minor stress-induced splicing changes, with observations reflecting findings from Arabidopsis studies.
• Genotypic Variability in Splicing: Identification of distinctive splicing features between grape genotypes, including variation in Serine/Arginine-rich splicing factors relevant to evolutionary and selective-pressure studies.

Scientific Applications:

• Gene prediction and annotation refinement: Use of RNAseq-informed annotations and new gene models to improve grape genome annotations.
• Functional genomics and transcriptomics: Analysis of AS patterns, isoform expression, and intron retention to study gene regulation.
• Comparative genomics across genotypes: Comparison of splicing features and splicing-factor variation between grape genotypes.
• Regulatory network exploration: Investigation of interactions between alternative splicing, miRNA target site modulation, and Serine/Arginine-rich splicing factors.

Methodology:

RNAseq analyses of 124 SOLiD experiments, BLAST sequence similarity searches, genome browser-based genomic context inspection, and gene prediction updates informed by RNAseq data.