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Title: | A comprehensive assessment of the transcriptome of cork oak (Quercus suber) through EST sequencing |
Author: | Pereira-Leal, Jose B. Abreu, Isabel A. Alabca, Claudia S. Almeida, Maria Helena Almeida, Paulo Almeida, Tania Amorim, Maria Isabel Araujo, Susana Azevedo, Herlander Badia, Aleix Batista, Dora Bohn, Andreas Capote, Tiago Carrasquinho, Isabel Chaves, Ines Coelho, Ana Cristina Ribeiro Costa, Maria Manuela Costa, Rita Cravador, Alfredo Egas, Conceicao Faro, Carlos Fortes, Ana M. Fortunato, Ana S. Gaspar, Maria Joao Goncalves, Sonia Graca, Jose Horta, Marilia Inacio, Vera Leitao, Jose M. Lino-Neto, Teresa Marum, Liliana Matos, Jose Mendonca, Diogo Miguel, Andreia Miguel, Celia M. Morais-Cecilio, Leonor Neves, Isabel Nobrega, Filomena Oliveira, Maria Margarida Oliveira, Rute Pais, Maria Salome Paiva, Jorge A. Paulo, Octavio S. Pinheiro, Miguel Raimundo, Joao A. P. Ramalho, Jose C. Ribeiro, Ana I. Ribeiro, Teresa Rocheta, Margarida Rodrigues, Ana Isabel Rodrigues, Jose C. Saibo, Nelson J. M. Santo, Tatiana E. Santos, Ana Margarida Sa-Pereira, Paula Sebastiana, Monica Simoes, Fernanda Sobral, Romulo S. Tavares, Rui Teixeira, Rita Varela, Carolina Veloso, Maria Manuela Ricardo, Candido P. P. |
Keywords: | PHYTOPHTHORA-CINNAMOMI PROTEIN GENOME ILEX PORTUGAL INTERPRO DISEASE MARKERS PLANTS TOOL |
Issue Date: | 2014 |
Publisher: | BIOMED CENTRAL LTD |
Abstract: | Background: Cork oak (Quercus suber) is one of the rare trees with the ability to produce cork, a material widely used to make wine bottle stoppers, flooring and insulation materials, among many other uses. The molecular mechanisms of cork formation are still poorly understood, in great part due to the difficulty in studying a species with a long life-cycle and for which there is scarce molecular/genomic information. Cork oak forests are of great ecological importance and represent a major economic and social resource in Southern Europe and Northern Africa. However, global warming is threatening the cork oak forests by imposing thermal, hydric and many types of novel biotic stresses. Despite the economic and social value of the Q. suber species, few genomic resources have been developed, useful for biotechnological applications and improved forest management. Results: We generated in excess of 7 million sequence reads, by pyrosequencing 21 normalized cDNA libraries derived from multiple Q. suber tissues and organs, developmental stages and physiological conditions. We deployed a stringent sequence processing and assembly pipeline that resulted in the identification of similar to 159,000 unigenes. These were annotated according to their similarity to known plant genes, to known Interpro domains, GO classes and E.C. numbers. The phylogenetic extent of this ESTs set was investigated, and we found that cork oak revealed a significant new gene space that is not covered by other model species or EST sequencing projects. The raw data, as well as the full annotated assembly, are now available to the community in a dedicated web portal at www.corkoakdb.org. Conclusions: This genomic resource represents the first trancriptome study in a cork producing species. It can be explored to develop new tools and approaches to understand stress responses and developmental processes in forest trees, as well as the molecular cascades underlying cork differentiation and disease response. |
Peer review: | yes |
URI: | http://hdl.handle.net/10773/20246 |
DOI: | 10.1186/1471-2164-15-371 |
ISSN: | 1471-2164 |
Publisher Version: | 10.1186/1471-2164-15-371 |
Appears in Collections: | CICECO - Artigos |
Files in This Item:
File | Description | Size | Format | |
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A comprehensive assessment of the transcriptome of cork oak (Quercus suber) through EST sequencing_10.11861471-2164-15-371.pdf | 1.46 MB | Adobe PDF | View/Open |
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