Characterizing the grape transcriptome: Analysis of ESTs from multiple Vitis species and development of a compendium of gene expression during berry development.

• Author(s): Cook, Douglas;
• Abstract: We report the analysis and annotation of 146,075 expressed sequenced tags (ESTs) from Vitis species. The majority of these sequences were derived from different cultivars of Vitis vinifera, comprising an estimated 25,746 unique contig and singleton sequences that survey transcription in various tissues, developmental stages, and responses to biotic and abiotic stress. Putatively homologous proteins were identified for over 17,752 of the transcripts, with 1,962 transcripts further subdivided into one or more gene ontology categories. A simple structured vocabulary, with modules for plant genotype, plant development, and stress, was developed to describe the relationship between individual ESTs and cDNA libraries; the resulting vocabulary provides query terms to facilitate data mining within the context of a relational database. As a measure of the extent to which characterized metabolic pathways were encompassed by the dataset, we searched for homologs of the enzymes leading from glycolysis, through the oxidative/non-oxidative pentose phosphate pathway, and into the general phenylpropanoid pathway. Homologs were identified for 65 of these 77 enzymes, with 86% of enzymatic steps represented by paralogous genes. Differentially expressed transcripts were identified by means of a stringent believability index cutoff of ≥98.4%. Correlation analysis and two-dimensional hierarchical clustering grouped these transcripts according to similarity of expression. In the broadest analysis, 693 differentially transcripts were identified across twenty-nine cDNA libraries, representing a range of developmental and stress conditions. The groupings revealed expected associations between plant developmental stages and tissue types, with the notable exception of abiotic stress treatments. A more focused analysis on flower and berry development identified 87 differentially transcripts and provides the basis for a compendium that relates gene expression and annotation to previously characterized aspects of berry development and physiology. Comparison with previously published results for select sequences, as well as correlation analysis between independent datasets, suggests that the inferred in silico patterns of expression are likely to be an accurate representation of transcript abundance for the conditions surveyed. Thus, the combined dataset reveals the in silico expression patterns for hundreds of genes in Vitis vinifera, the majority of which have not been previously studied within this species.
• Publication Date: Oct 2005
• Journal: Plant Physiology