A comprehensive assessment of the transcriptome of cork oak (Quercus suber) through EST sequencing

Springer Science and Business Media LLC - Tập 15 - Trang 1-14 - 2014
José B Pereira-Leal1, Isabel A Abreu2,3, Cláudia S Alabaça4, Maria Helena Almeida5, Paulo Almeida1, Tânia Almeida6,7, Maria Isabel Amorim8, Susana Araújo9,10,11, Herlânder Azevedo12,13, Aleix Badia14,15, Dora Batista16, Andreas Bohn14,15, Tiago Capote6,7, Isabel Carrasquinho17, Inês Chaves18,19,20,21, Ana Cristina Coelho22, Maria Manuela Ribeiro Costa12, Rita Costa17, Alfredo Cravador23, Conceição Egas24, Carlos Faro24, Ana M Fortes25, Ana S Fortunato26, Maria João Gaspar27,28, Sónia Gonçalves6,7, José Graça28, Marília Horta23, Vera Inácio29, José M Leitão4, Teresa Lino-Neto12, Liliana Marum20,21, José Matos17, Diogo Mendonça17, Andreia Miguel20,21, Célia M Miguel20,21, Leonor Morais-Cecílio29, Isabel Neves1, Filomena Nóbrega17, Maria Margarida Oliveira2,3, Rute Oliveira12, Maria Salomé Pais30, Jorge A Paiva9,10,31, Octávio S Paulo32, Miguel Pinheiro24, João AP Raimundo12, José C Ramalho26, Ana I Ribeiro26, Teresa Ribeiro6,7,29, Margarida Rocheta29, Ana Isabel Rodrigues5, José C Rodrigues31, Nelson JM Saibo2,3, Tatiana E Santo4, Ana Margarida Santos1,2,3, Paula Sá-Pereira17, Mónica Sebastiana30, Fernanda Simões17, Rómulo S Sobral12, Rui Tavares12, Rita Teixeira5, Carolina Varela17, Maria Manuela Veloso17, Cândido PP Ricardo18,19
1Instituto Gulbenkian de Ciência, Oeiras, Portugal
2Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Genomics of Plant Stress Lab, Oeiras, Portugal
3Instituto de Biologia Experimental e Tecnológica, Genomics of Plant Stress Lab, Oeiras, Portugal
4Laboratory of Genomics and Genetic Improvement, BioFIG, FCT, Universidade do Algarve, Faro, Portugal
5Centro Estudos Florestais (CEF), Instituto Superior de Agronomia, Universidade de Lisboa, Tapada da Ajuda, Portugal
6Centro de Biotecnologia Agrícola e Agro-Alimentar do Alentejo (CEBAL)/Instituto Politécnico de Beja (IPBeja), Beja, Portugal
7Centre for Research in Ceramics & Composite Materials (CICECO), Universidade de Aveiro, Campus Universitário de Santiago, Aveiro, Portugal
8Faculdade de Ciências, Universidade do Porto, Porto, Portugal
9Instituto de Biologia Experimental e Tecnológica, Plant Cell Biotecnology Lab, Oeiras, Portugal
10Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Plant Cell Biotecnology Lab, Oeiras, Portugal
11Instituto de Investigação Científica Tropical (IICT), BIOTROP/Veterinária e Zootecnia, Lisboa, Portugal
12Centre for Biodiversity, Functional & Integrative Genomics (BioFIG), Plant Functional Biology Centre, Universidade do Minho, Campus de Gualtar, Braga, Portugal
13CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Vairão, Portugal
14Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Systems Biodynamics Lab, Oeiras, Portugal
15Instituto de Biologia Experimental e Tecnológica, Systems Biodynamics Lab, Oeiras, Portugal
16Centro de Investigação das Ferrugens do Cafeeiro/BioTrop, Instituto de Investigação Científica Tropical, Oeiras, Portugal
17INIAV- Instituto Nacional de Investigação Agrária e Veterinária, IP, Quinta do Marquês, Oeiras, Portugal
18Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Plant Biochemistry Lab, Oeiras, Portugal
19Instituto de Biologia Experimental e Tecnológica, Plant Biochemistry Lab, Oeiras, Portugal
20Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Forest Biotech Lab, Oeiras, Portugal
21Instituto de Biologia Experimental e Tecnológica, Forest Biotech Lab, Oeiras, Portugal
22Centro de Electrónica, Optoelectrónica e Telecomunicações (CEOT), Universidade do Algarve, Campus de Gambelas, Faro, Portugal
23Institute for Biotechnology and Bioengineering - Centre of Genomics and Biotechnology (IBB-CGB), Plant and Animal Genomic Group, Universidade do Algarve - Campus de Gambelas, Faro, Portugal
24Biocant, Parque Tecnológico de Cantanhede, Cantanhede, Portugal
25Centre for Biodiversity, Functional & Integrative Genomics (BioFIG), Faculdade de Ciências da Universidade de Lisboa, Lisboa, Portugal
26Unidade de Ecofisiologia, Bioquímica e Biotecnologia Vegetal/BioTrop, Instituto de Investigação Científica Tropical, Oeiras, Portugal
27Departamento Genética e Biotecnologia, Univ. Trás-os-Monte e Alto Douro, Vila Real, Portugal
28CEF, ISA Technical University Lisbon, Tapada da Ajuda, Lisboa, Portugal
29Centro Botânica Aplicada Agricultura (CBAA), Instituto Superior de Agronomia, Universidade Técnica de Lisboa, Tapada da Ajuda, Lisboa, Portugal
30Centre for Biodiversity, Functional & Integrative Genomics (BioFIG), Plant Systems Biology Lab, Faculdade de Ciências da Universidade de Lisboa, Lisboa, Portugal
31Instituto de Investigação Científica Tropical (IICT), BIOTROP/Florestas e dos Produtos Florestais, Tapada da Ajuda, Lisboa, Portugal
32Centro de Biologia Ambiental, Faculdade de Ciências da Universidade de Lisboa, Campo Grande, Lisboa, Portugal

Tóm tắt

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. 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 ~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 http://www.corkoakdb.org . 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.

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