Tags

Type your tag names separated by a space and hit enter

Generation of ESTs in Vitis vinifera wine grape (Cabernet Sauvignon) and table grape (Muscat Hamburg) and discovery of new candidate genes with potential roles in berry development.
Gene. 2007 Nov 01; 402(1-2):40-50.GENE

Abstract

We report the generation and analysis of a total of 77,583 expressed sequence tags (ESTs) from two grapevine (Vitis vinifera L.) cultivars, Cabernet Sauvignon (wine grape) and Muscat Hamburg (table grape) with a focus on EST sequence quality and assembly optimization. The majority of the ESTs were derived from normalized cDNA libraries representing berry pericarp and seed developmental series, pooled non-berry tissues including root, flower, and leaf in Cabernet Sauvignon, and pooled tissues of berry, seed, and flower in Muscat Hamburg. EST and unigene sequence quality were determined by computational filtering coupled with small-scale contig reassembly, manual review, and BLAST analyses. EST assembly was optimized to better discriminate among closely related paralogs using two independent grape sequence sets, a previously published set of Vitis spp. gene families and our EST dataset derived from pooled leaf, flower, and root tissues of Cabernet Sauvignon. Sequence assembly within individual libraries indicated that those prepared from pooled tissues contributed the most to gene discovery. Annotations based upon searches against multiple databases including tomato and strawberry sequences helped to identify putative functions of ESTs and unigenes, particularly with respect to fleshy fruit development. Sequence comparison among the three wine grape libraries identified a number of genes preferentially expressed in the pericarp tissue, including transcription factors, receptor-like protein kinases, and hexose transporters. Gene ontology (GO) classification in the biological process aspect showed that GO categories corresponding to 'transport' and 'cell organization and biogenesis', which are associated with metabolite movement and cell wall structural changes during berry ripening, were higher in pericarp than in other tissues in the wine grape studied. The sequence data were used to characterize potential roles of new genes in berry development and composition.

Links

Publisher Full Text

Authors+Show Affiliations

Peng FY
Wine Research Centre, Faculty of Land and Food Systems, University of British Columbia, 2205 East Mall, Vancouver, British Columbia, Canada V6T 1Z4.
Reid KE
No affiliation info available
Liao N
No affiliation info available
Schlosser J
No affiliation info available
Lijavetzky D
No affiliation info available
Holt R
No affiliation info available
Martínez Zapater JM
No affiliation info available
Jones S
No affiliation info available
Marra M
No affiliation info available
Bohlmann J
No affiliation info available
Lund ST
No affiliation info available

MeSH

Expressed Sequence TagsFruitGene Expression Regulation, PlantGene LibraryGenes, PlantModels, BiologicalSequence Analysis, DNAVitis

Pub Type(s)

Comparative Study
Journal Article
Research Support, Non-U.S. Gov't

Language

eng

PubMed ID

17761391

Citation

Peng, Fred Y., et al. "Generation of ESTs in Vitis Vinifera Wine Grape (Cabernet Sauvignon) and Table Grape (Muscat Hamburg) and Discovery of New Candidate Genes With Potential Roles in Berry Development." Gene, vol. 402, no. 1-2, 2007, pp. 40-50.
Peng FY, Reid KE, Liao N, et al. Generation of ESTs in Vitis vinifera wine grape (Cabernet Sauvignon) and table grape (Muscat Hamburg) and discovery of new candidate genes with potential roles in berry development. Gene. 2007;402(1-2):40-50.
Peng, F. Y., Reid, K. E., Liao, N., Schlosser, J., Lijavetzky, D., Holt, R., Martínez Zapater, J. M., Jones, S., Marra, M., Bohlmann, J., & Lund, S. T. (2007). Generation of ESTs in Vitis vinifera wine grape (Cabernet Sauvignon) and table grape (Muscat Hamburg) and discovery of new candidate genes with potential roles in berry development. Gene, 402(1-2), 40-50.
Peng FY, et al. Generation of ESTs in Vitis Vinifera Wine Grape (Cabernet Sauvignon) and Table Grape (Muscat Hamburg) and Discovery of New Candidate Genes With Potential Roles in Berry Development. Gene. 2007 Nov 1;402(1-2):40-50. PubMed PMID: 17761391.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Generation of ESTs in Vitis vinifera wine grape (Cabernet Sauvignon) and table grape (Muscat Hamburg) and discovery of new candidate genes with potential roles in berry development. AU - Peng,Fred Y, AU - Reid,Karen E, AU - Liao,Nancy, AU - Schlosser,James, AU - Lijavetzky,Diego, AU - Holt,Robert, AU - Martínez Zapater,José M, AU - Jones,Steven, AU - Marra,Marco, AU - Bohlmann,Jörg, AU - Lund,Steven T, Y1 - 2007/07/31/ PY - 2007/03/08/received PY - 2007/06/26/revised PY - 2007/07/17/accepted PY - 2007/9/1/pubmed PY - 2007/12/13/medline PY - 2007/9/1/entrez SP - 40 EP - 50 JF - Gene JO - Gene VL - 402 IS - 1-2 N2 - We report the generation and analysis of a total of 77,583 expressed sequence tags (ESTs) from two grapevine (Vitis vinifera L.) cultivars, Cabernet Sauvignon (wine grape) and Muscat Hamburg (table grape) with a focus on EST sequence quality and assembly optimization. The majority of the ESTs were derived from normalized cDNA libraries representing berry pericarp and seed developmental series, pooled non-berry tissues including root, flower, and leaf in Cabernet Sauvignon, and pooled tissues of berry, seed, and flower in Muscat Hamburg. EST and unigene sequence quality were determined by computational filtering coupled with small-scale contig reassembly, manual review, and BLAST analyses. EST assembly was optimized to better discriminate among closely related paralogs using two independent grape sequence sets, a previously published set of Vitis spp. gene families and our EST dataset derived from pooled leaf, flower, and root tissues of Cabernet Sauvignon. Sequence assembly within individual libraries indicated that those prepared from pooled tissues contributed the most to gene discovery. Annotations based upon searches against multiple databases including tomato and strawberry sequences helped to identify putative functions of ESTs and unigenes, particularly with respect to fleshy fruit development. Sequence comparison among the three wine grape libraries identified a number of genes preferentially expressed in the pericarp tissue, including transcription factors, receptor-like protein kinases, and hexose transporters. Gene ontology (GO) classification in the biological process aspect showed that GO categories corresponding to 'transport' and 'cell organization and biogenesis', which are associated with metabolite movement and cell wall structural changes during berry ripening, were higher in pericarp than in other tissues in the wine grape studied. The sequence data were used to characterize potential roles of new genes in berry development and composition. SN - 0378-1119 UR - https://www.unboundmedicine.com/medline/citation/17761391/Generation_of_ESTs_in_Vitis_vinifera_wine_grape__Cabernet_Sauvignon__and_table_grape__Muscat_Hamburg__and_discovery_of_new_candidate_genes_with_potential_roles_in_berry_development_ L2 - https://linkinghub.elsevier.com/retrieve/pii/S0378-1119(07)00397-6 DB - PRIME DP - Unbound Medicine ER -