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

  1. Peng, F.Y. 3
  2. Reid, K.E. 3
  3. Liao, N. 1
  4. Schlosser, J. 3
  5. Lijavetzky, D. 2
  6. Holt, R. 1
  7. Martínez Zapater, J.M. 2
  8. Jones, S. 1
  9. Marra, M. 1
  10. Bohlmann, J. 3
  11. Lund, S.T. 3
  1. 1 Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, 100-570 West 7th Ave, Vancouver, BC V5Z 4S6, Canada
  2. 2 Centro Nacional de Biotecnología
    info

    Centro Nacional de Biotecnología

    Madrid, España

    ROR https://ror.org/015w4v032

  3. 3 University of British Columbia
    info

    University of British Columbia

    Vancouver, Canadá

    ROR https://ror.org/03rmrcq20

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Revista:
Gene

ISSN: 0378-1119

Ano de publicación: 2007

Volume: 402

Número: 1-2

Páxinas: 40-50

Tipo: Artigo

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DOI: 10.1016/J.GENE.2007.07.016 PMID: 17761391 SCOPUS: 2-s2.0-34548785463 GOOGLE SCHOLAR

Outras publicacións en: Gene

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Resumo

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. © 2007 Elsevier B.V. All rights reserved.