Dataset Information

Comparative expression profiling in grape (Vitis vinifera) berries derived from frequency analysis of ESTs and MPSS signatures.

ABSTRACT: BACKGROUND: Vitis vinifera (V. vinifera) is the primary grape species cultivated for wine production, with an industry valued annually in the billions of dollars worldwide. In order to sustain and increase grape production, it is necessary to understand the genetic makeup of grape species. Here we performed mRNA profiling using Massively Parallel Signature Sequencing (MPSS) and combined it with available Expressed Sequence Tag (EST) data. These tag-based technologies, which do not require a priori knowledge of genomic sequence, are well-suited for transcriptional profiling. The sequence depth of MPSS allowed us to capture and quantify almost all the transcripts at a specific stage in the development of the grape berry. RESULTS: The number and relative abundance of transcripts from stage II grape berries was defined using Massively Parallel Signature Sequencing (MPSS). A total of 2,635,293 17-base and 2,259,286 20-base signatures were obtained, representing at least 30,737 and 26,878 distinct sequences. The average normalized abundance per signature was approximately 49 TPM (Transcripts Per Million). Comparisons of the MPSS signatures with available Vitis species' ESTs and a unigene set demonstrated that 6,430 distinct contigs and 2,190 singletons have a perfect match to at least one MPSS signature. Among the matched sequences, ESTs were identified from tissues other than berries or from berries at different developmental stages. Additional MPSS signatures not matching to known grape ESTs can extend our knowledge of the V. vinifera transcriptome, particularly when these data are used to assist in annotation of whole genome sequences from Vitis vinifera. CONCLUSION: The MPSS data presented here not only achieved a higher level of saturation than previous EST based analyses, but in doing so, expand the known set of transcripts of grape berries during the unique stage in development that immediately precedes the onset of ripening. The MPSS dataset also revealed evidence of antisense expression not previously reported in grapes but comparable to that reported in other plant species. Finally, we developed a novel web-based, public resource for utilization of the grape MPSS data [1].

SUBMITTER: Iandolino A

PROVIDER: S-EPMC2423195 | biostudies-literature | 2008

REPOSITORIES: biostudies-literature

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Comparative expression profiling in grape (Vitis vinifera) berries derived from frequency analysis of ESTs and MPSS signatures.

Iandolino Alberto A Nobuta Kan K da Silva Francisco Goes FG Cook Douglas R DR Meyers Blake C BC

BMC plant biology 20080512

<h4>Background</h4>Vitis vinifera (V. vinifera) is the primary grape species cultivated for wine production, with an industry valued annually in the billions of dollars worldwide. In order to sustain and increase grape production, it is necessary to understand the genetic makeup of grape species. Here we performed mRNA profiling using Massively Parallel Signature Sequencing (MPSS) and combined it with available Expressed Sequence Tag (EST) data. These tag-based technologies, which do not require ...[more]

PMID: 18474095

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Project description:Vitis vinifera cv. Koshu is an indigenous grape cultivar that has been cultivated for more than a thousand years in Japan and one of the most important cultivars in white winemaking. To improve Koshu wine quality, it is necessary to identify the metabolites in Koshu berry. We conducted a comprehensive and comparative lipidome analysis of Koshu and Pinot Noir berries cultivated in the same location in Japan using GC-MS/MS for fatty acids and LC-MS for glycerolipids and glycerophospholipids. Koshu skins and juices contained 22 and 19 fatty acids, respectively, whereas 23 and 20 fatty acids were detected in Pinot Noir skins and juices. C22:6n3 and C24:0 contents in Koshu skins were two and three times higher than those in Pinot Noir skins. C24:0 content in Koshu juices was also higher than that in Pinot Noir juices. Forty-nine lipid components (six digalactosyldiacylglycerols, one monogalactosyldiacylglycerol, 10 phosphatidylcholines, 12 phosphatidylethanolamines, and 20 triglycerides) were detected in Pinot Noir and Koshu skins. Strong peaks were observed for MGDG 36:6, DGDG 36:6, PC 34:2, PC 36:5, TG 54:6, TG 54:7, and TG 54:8 in Koshu skins. The contents of 36 of the 49 lipid components were significantly higher in Pinot Noir skins than Koshu skins. Pinot Noir skins contained more lipids whose alkyl chains have more than 18 carbons than Koshu skins. Further analysis of both lipid profiles revealed that the number of double bonds in a fatty acid molecule in Pinot Noir skins and juices was significantly larger than that in Koshu skins and juices. A strong relationship exists between the heat requirement of grapevine cultivars and the level of fatty acid desaturation. C18-fatty acids were the major components in Koshu and Pinot Noir berries. The expression levels of C18-fatty acid desaturases regulated the accumulation of C18-unsaturated fatty acids in berry skins. The loss of C18:3 in Koshu berries at the end of ripening was observed. Koshu might effectively convert C18:3 into (Z)-hex-3-enal for the production of C6-aroma compounds. These findings by the lipidome analysis are expected to contribute to the improvement of Koshu wine aroma and breeding strategies of cold-tolerant Koshu grapevines.

Dataset Information

Comparative expression profiling in grape (Vitis vinifera) berries derived from frequency analysis of ESTs and MPSS signatures.

Publications

Comparative expression profiling in grape (Vitis vinifera) berries derived from frequency analysis of ESTs and MPSS signatures.

Similar Datasets

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