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Open Access Research article

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

José B Pereira-Leal1*, Isabel A Abreu23, Cláudia S Alabaça4, Maria Helena Almeida5, Paulo Almeida1, Tânia Almeida67, Maria Isabel Amorim8, Susana Araújo10119, Herlânder Azevedo1232, Aleix Badia1314, Dora Batista15, Andreas Bohn1314, Tiago Capote67, Isabel Carrasquinho16, Inês Chaves17181920, Ana Cristina Coelho21, Maria Manuela Ribeiro Costa12, Rita Costa16, Alfredo Cravador22, Conceição Egas23, Carlos Faro23, Ana M Fortes24, Ana S Fortunato25, Maria João Gaspar2627, Sónia Gonçalves67, José Graça27, Marília Horta22, Vera Inácio28, José M Leitão4, Teresa Lino-Neto12, Liliana Marum1920, José Matos16, Diogo Mendonça16, Andreia Miguel1920, Célia M Miguel1920, Leonor Morais-Cecílio28, Isabel Neves1, Filomena Nóbrega16, Maria Margarida Oliveira23, Rute Oliveira12, Maria Salomé Pais29, Jorge A Paiva10309, Octávio S Paulo31, Miguel Pinheiro23, João AP Raimundo12, José C Ramalho25, Ana I Ribeiro25, Teresa Ribeiro2867, Margarida Rocheta28, Ana Isabel Rodrigues5, José C Rodrigues30, Nelson JM Saibo23, Tatiana E Santo4, Ana Margarida Santos123, Paula Sá-Pereira16, Mónica Sebastiana29, Fernanda Simões16, Rómulo S Sobral12, Rui Tavares12, Rita Teixeira5, Carolina Varela16, Maria Manuela Veloso16 and Cândido PP Ricardo1718

Author Affiliations

1 Instituto Gulbenkian de Ciência, Rua da Quinta Grande 6, Oeiras 2780-156, Portugal

2 Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Genomics of Plant Stress Lab, Av. da República, Oeiras 2780-157, Portugal

3 Instituto de Biologia Experimental e Tecnológica, Genomics of Plant Stress Lab, Apartado 12, Oeiras 2781-901, Portugal

4 Laboratory of Genomics and Genetic Improvement, BioFIG, FCT, Universidade do Algarve, E.8, Campus de Gambelas, Faro 8300, Portugal

5 Centro Estudos Florestais (CEF), Instituto Superior de Agronomia, Universidade de Lisboa, Tapada da Ajuda, Lisboa 1349-017, Portugal

6 Centro de Biotecnologia Agrícola e Agro-Alimentar do Alentejo (CEBAL)/ Instituto Politécnico de Beja (IPBeja), Beja 7801-908, Portugal

7 Centre for Research in Ceramics & Composite Materials (CICECO), Universidade de Aveiro, Campus Universitário de Santiago, Aveiro 3810-193, Portugal

8 Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre, s/n, FC4, Porto 4169-007, Portugal

9 Instituto de Biologia Experimental e Tecnológica, Plant Cell Biotecnology Lab, Apartado 12, Oeiras 2781-901, Portugal

10 Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Plant Cell Biotecnology Lab, Av. da República, Oeiras 2780-157, Portugal

11 Instituto de Investigação Científica Tropical (IICT), BIOTROP/Veterinária e Zootecnia, R. da Junqueira, 86 - 1, Lisboa 1300-344, Portugal

12 Centre for Biodiversity, Functional & Integrative Genomics (BioFIG), Plant Functional Biology Centre, Universidade do Minho, Campus de Gualtar, Braga 4710-057, Portugal

13 Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Systems Biodynamics Lab, Av. da República, 2780-157 Oeiras, Portugal

14 Instituto de Biologia Experimental e Tecnológica, Systems Biodynamics Lab, Apartado 12, Oeiras 2781-901, Portugal

15 Centro de Investigação das Ferrugens do Cafeeiro/BioTrop, Instituto de Investigação Científica Tropical, Quinta do Marquês, Oeiras 2784-505, Portugal

16 INIAV- Instituto Nacional de Investigação Agrária e Veterinária, IP, Quinta do Marquês, Oeiras 2780-159, Portugal

17 Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Plant Biochemistry Lab, Av. da República, Oeiras 2780-157, Portugal

18 Instituto de Biologia Experimental e Tecnológica, Plant Biochemistry Lab, Apartado 12, Oeiras 2781-901, Portugal

19 Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Forest Biotech Lab, Av. da República, Oeiras 2780-157, Portugal

20 Instituto de Biologia Experimental e Tecnológica, Forest Biotech Lab, Apartado 12, Oeiras 2781-901, Portugal

21 Centro de Electrónica, Optoelectrónica e Telecomunicações (CEOT), Universidade do Algarve, Campus de Gambelas, Faro 8005-139, Portugal

22 Institute for Biotechnology and Bioengineering - Centre of Genomics and Biotechnology (IBB-CGB), Plant and Animal Genomic Group, Universidade do Algarve - Campus de Gambelas, Faro 8005-139, Portugal

23 Biocant, Parque Tecnológico de Cantanhede, Cantanhede 3060 - 197, Portugal

24 Centre for Biodiversity, Functional & Integrative Genomics (BioFIG), Faculdade de Ciências da Universidade de Lisboa, Lisboa 1749-016, Portugal

25 Unidade de Ecofisiologia, Bioquímica e Biotecnologia Vegetal/BioTrop, Instituto de Investigação Científica Tropical, Quinta do Marquês, Av. da República, Oeiras 2784-505, Portugal

26 Departamento Genética e Biotecnologia, Univ. Trás-os-Monte e Alto Douro, Vila Real 5001-801, Portugal

27 CEF, ISA Technical University Lisbon, Tapada da Ajuda, Lisboa 1349-017, Portugal

28 Centro Botânica Aplicada Agricultura (CBAA), Instituto Superior de Agronomia, Universidade Técnica de Lisboa, Tapada da Ajuda, Lisboa 1349-017, Portugal

29 Centre for Biodiversity, Functional & Integrative Genomics (BioFIG), Plant Systems Biology Lab, Faculdade de Ciências da Universidade de Lisboa, Lisboa 1749-016, Portugal

30 Instituto de Investigação Científica Tropical (IICT), BIOTROP/Florestas e dos Produtos Florestais, Tapada da Ajuda, Lisboa 1349-017, Portugal

31 Centro de Biologia Ambiental, Faculdade de Ciências da Universidade de Lisboa, Campo Grande, Lisboa 1749-016, Portugal

32 Current Address: CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus Agrário de Vairão, Vairão 4485-661, Portugal

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BMC Genomics 2014, 15:371  doi:10.1186/1471-2164-15-371

Published: 15 May 2014

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 ~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 webcite.

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.