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

Jose B. Pereira-Leal; Isabel A. Abreu; Claudia S. Alabca; Maria Helena Almeida; Paulo Almeida; Tania Almeida; Maria Isabel Amorim; Susana Araujo; Herlander Azevedo; Aleix Badia; Dora Batista; Andreas Bohn; Tiago Capote; Isabel Carrasquinho; Ines Chaves; Ana Cristina Coelho; Maria Manuela Ribeiro Costa; Rita Costa; Alfredo Cravador; Conceicao Egas; Carlos Faro; Ana M. Fortes; Ana S. Fortunato; Maria Joao Gaspar; Sonia Goncalves; Jose Graca; Marilia Horta; Vera Inacio; Jose M. Leitao; Teresa Lino-Neto; Liliana Marum; Jose Matos; Diogo Mendonca; Andreia Miguel; Celia M. Miguel; Leonor Morais-Cecilio; Isabel Neves; Filomena Nobrega; Maria Margarida Oliveira; Rute Oliveira; Maria Salome Pais; Jorge A. Paiva; Octavio S. Paulo; Miguel Pinheiro; Joao A. P. Raimundo; Jose C. Ramalho; Ana I. Ribeiro; Teresa Ribeiro; Margarida Rocheta; Ana Isabel Rodrigues; Jose C. Rodrigues; Nelson J. M. Saibo; Tatiana E. Santo; Ana Margarida Santos; Paula Sa-Pereira; Monica Sebastiana; Fernanda Simoes; Romulo S. Sobral; Rui Tavares; Rita Teixeira; Carolina Varela; Maria Manuela Veloso; Candido P. P. Ricardo

doi:10.1186/1471-2164-15-371

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

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

Jose B. Pereira-Leal, Isabel A. Abreu, Claudia S. Alabca, Maria Helena Almeida, Paulo Almeida, Tania Almeida, Maria Isabel Amorim, Susana Araujo, Herlander Azevedo, Aleix Badia, …

BMC genomics, Vol.15(1), pp.1-14

15/05/2014

DOI: https://doi.org/10.1186/1471-2164-15-371

PMID: 24885229

Résumé

Biotechnology & Applied Microbiology

Genetics & Heredity

Life Sciences & Biomedicine

Science & Technology

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.

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Titre: A comprehensive assessment of the transcriptome of cork oak (Quercus suber) through EST sequencing
Créateurs - sans rôle: Jose B. Pereira-Leal - Inst Gulbenkian Ciencias, P-2780156 Oeiras, Portugal
Isabel A. Abreu - Univ Nova Lisboa, Inst Tecnol Quim & Biol, Genom Plant Stress Lab, P-2780157 Oeiras, Portugal
Claudia S. Alabca - Univ Algarve, FCT, BioFIG, Lab Genom & Genet Improvement, P-8300 Faro, Portugal
Maria Helena Almeida - Univ Lisbon, Inst Super Agron, Ctr Estudos Florestais, P-1349017 Lisbon, Portugal
Paulo Almeida - Inst Gulbenkian Ciencias, P-2780156 Oeiras, Portugal
Tania Almeida - Inst Politecn Beja IPBeja, Ctr Biotecnol Agr & Agroalimentar Alentejo CEBAL, P-7801908 Beja, Portugal
Maria Isabel Amorim - Univ Porto, Fac Ciencias, P-4169007 Oporto, Portugal
Susana Araujo - Inst Biol Expt & Tecnol, Plant Cell Biotecnol Lab, P-2781901 Oeiras, Portugal
Herlander Azevedo - Univ Minho, Plant Funct Biol Ctr, Ctr Biodivers Funct & Integrat Genom BioFIG, P-4710057 Braga, Portugal
Aleix Badia - Univ Nova Lisboa, Inst Tecnol Quim & Biol, Syst Biodynam Lab, P-2780157 Oeiras, Portugal
Dora Batista - Ctr Invest Ferrugens Cafeeiro BioTrop, Inst Invest Cient Trop, P-2784505 Oeiras, Portugal
Andreas Bohn - Univ Nova Lisboa, Inst Tecnol Quim & Biol, Syst Biodynam Lab, P-2780157 Oeiras, Portugal
Tiago Capote - Inst Politecn Beja IPBeja, Ctr Biotecnol Agr & Agroalimentar Alentejo CEBAL, P-7801908 Beja, Portugal
Isabel Carrasquinho - INIAV Inst Nacl Invest Agr & Vet, P-2780159 Oeiras, Portugal
Ines Chaves - Univ Nova Lisboa, Plant Biochem Lab, Inst Tecnol Quim & Biol, P-2780157 Oeiras, Portugal
Ana Cristina Coelho - Univ Algarve, Ctr Elect Optoelect & Telecomunicacoes, P-8005139 Faro, Portugal
Maria Manuela Ribeiro Costa - Univ Minho, Plant Funct Biol Ctr, Ctr Biodivers Funct & Integrat Genom BioFIG, P-4710057 Braga, Portugal
Rita Costa - INIAV Inst Nacl Invest Agr & Vet, P-2780159 Oeiras, Portugal
Alfredo Cravador - Univ Algarve, Inst Biotechnol & Bioengn, Ctr Genom & Biotechnol, Plant & Anim Genom Grp, P-8005139 Faro, Portugal
Conceicao Egas - Biocant, P-3060197 Cantanhede, Portugal
Carlos Faro - Biocant, P-3060197 Cantanhede, Portugal
Ana M. Fortes - Univ Lisbon, Fac Ciencias, Ctr Biodivers Funct & Integrat Genom BioFIG, P-1749016 Lisbon, Portugal
Ana S. Fortunato - Inst Invest Cient Trop, Unidade Ecofisiol Bioquim & Biotecnol Vegetal Bio, P-2784505 Oeiras, Portugal
Maria Joao Gaspar - Univ Tros Os Monte & Alto Douro, Dept Genet & Biotecnol, P-5001801 Vila Real, Portugal
Sonia Goncalves - Inst Politecn Beja IPBeja, Ctr Biotecnol Agr & Agroalimentar Alentejo CEBAL, P-7801908 Beja, Portugal
Jose Graca - ISA Tech Univ Lisbon, CEF, P-1349017 Lisbon, Portugal
Marilia Horta - Univ Algarve, Inst Biotechnol & Bioengn, Ctr Genom & Biotechnol, Plant & Anim Genom Grp, P-8005139 Faro, Portugal
Vera Inacio - Univ Tecn Lisboa, Inst Super Agron, Ctr Bot Aplicada Agr, P-1349017 Lisbon, Portugal
Jose M. Leitao - Univ Algarve, FCT, BioFIG, Lab Genom & Genet Improvement, P-8300 Faro, Portugal
Teresa Lino-Neto - Univ Minho, Plant Funct Biol Ctr, Ctr Biodivers Funct & Integrat Genom BioFIG, P-4710057 Braga, Portugal
Liliana Marum - Univ Nova Lisboa, Inst Tecnol Quim & Biol, Forest Biotech Lab, P-2780157 Oeiras, Portugal
Jose Matos - INIAV Inst Nacl Invest Agr & Vet, P-2780159 Oeiras, Portugal
Diogo Mendonca - INIAV Inst Nacl Invest Agr & Vet, P-2780159 Oeiras, Portugal
Andreia Miguel - Univ Nova Lisboa, Inst Tecnol Quim & Biol, Forest Biotech Lab, P-2780157 Oeiras, Portugal
Celia M. Miguel - Univ Nova Lisboa, Inst Tecnol Quim & Biol, Forest Biotech Lab, P-2780157 Oeiras, Portugal
Leonor Morais-Cecilio - Univ Tecn Lisboa, Inst Super Agron, Ctr Bot Aplicada Agr, P-1349017 Lisbon, Portugal
Isabel Neves
Filomena Nobrega - INIAV Inst Nacl Invest Agr & Vet, P-2780159 Oeiras, Portugal
Maria Margarida Oliveira - Univ Nova Lisboa, Inst Tecnol Quim & Biol, Genom Plant Stress Lab, P-2780157 Oeiras, Portugal
Rute Oliveira - Univ Minho, Plant Funct Biol Ctr, Ctr Biodivers Funct & Integrat Genom BioFIG, P-4710057 Braga, Portugal
Maria Salome Pais - Univ Lisbon, Fac Ciencias, Plant Syst Biol Lab, Ctr Biodivers Funct & Integrat Genom BioFIG, P-1749016 Lisbon, Portugal
Jorge A. Paiva - Inst Biol Expt & Tecnol, Plant Cell Biotecnol Lab, P-2781901 Oeiras, Portugal
Octavio S. Paulo - Univ Lisbon, Fac Ciencias, Ctr Biol Ambiental, P-1749016 Lisbon, Portugal
Miguel Pinheiro - Biocant, P-3060197 Cantanhede, Portugal
Joao A. P. Raimundo - Univ Minho, Plant Funct Biol Ctr, Ctr Biodivers Funct & Integrat Genom BioFIG, P-4710057 Braga, Portugal
Jose C. Ramalho - Inst Invest Cient Trop, Unidade Ecofisiol Bioquim & Biotecnol Vegetal Bio, P-2784505 Oeiras, Portugal
Ana I. Ribeiro - Inst Invest Cient Trop, Unidade Ecofisiol Bioquim & Biotecnol Vegetal Bio, P-2784505 Oeiras, Portugal
Teresa Ribeiro - Univ Aveiro, Ctr Res Ceram & Composite Mat CICECO, P-3810193 Aveiro, Portugal
Margarida Rocheta - Univ Tecn Lisboa, Inst Super Agron, Ctr Bot Aplicada Agr, P-1349017 Lisbon, Portugal
Ana Isabel Rodrigues - Univ Lisbon, Inst Super Agron, Ctr Estudos Florestais, P-1349017 Lisbon, Portugal
Jose C. Rodrigues - Inst Invest Cient Trop, BIOTROP Florestas & Prod Florestais, P-1349017 Lisbon, Portugal
Nelson J. M. Saibo - Univ Nova Lisboa, Inst Tecnol Quim & Biol, Genom Plant Stress Lab, P-2780157 Oeiras, Portugal
Tatiana E. Santo - Univ Algarve, FCT, BioFIG, Lab Genom & Genet Improvement, P-8300 Faro, Portugal
Ana Margarida Santos - Inst Gulbenkian Ciencias, P-2780156 Oeiras, Portugal
Paula Sa-Pereira - INIAV Inst Nacl Invest Agr & Vet, P-2780159 Oeiras, Portugal
Monica Sebastiana - Univ Lisbon, Fac Ciencias, Plant Syst Biol Lab, Ctr Biodivers Funct & Integrat Genom BioFIG, P-1749016 Lisbon, Portugal
Fernanda Simoes - INIAV Inst Nacl Invest Agr & Vet, P-2780159 Oeiras, Portugal
Romulo S. Sobral - Univ Minho, Plant Funct Biol Ctr, Ctr Biodivers Funct & Integrat Genom BioFIG, P-4710057 Braga, Portugal
Rui Tavares - Univ Minho, Plant Funct Biol Ctr, Ctr Biodivers Funct & Integrat Genom BioFIG, P-4710057 Braga, Portugal
Rita Teixeira
Carolina Varela - INIAV Inst Nacl Invest Agr & Vet, P-2780159 Oeiras, Portugal
Maria Manuela Veloso - INIAV Inst Nacl Invest Agr & Vet, P-2780159 Oeiras, Portugal
Candido P. P. Ricardo - Univ Nova Lisboa, Plant Biochem Lab, Inst Tecnol Quim & Biol, P-2780157 Oeiras, Portugal
Détails de publication: BMC genomics, Vol.15(1), pp.1-14
Éditeur: Springer Nature
Nombre de pages: 14
Note de subvention: SFRH/BD/44410/2008; SFRH/BD/69785/2010; SFRH/BPD/20833/2004; SFRH/BPD/47563/2008; SFRH/BPD/63213/2009; SFRH/BPD/47679/2008; SFRH/BD/44474/2008; SFRH/BPD/64905/2009; SFRH/BD/47450/2008; SFRH/BPD/25661/2005; PEst-OE/EQB/LA0004/2011 / "Fundacao para a Ciencia e a Tecnologia" (FCT); Fundacao para a Ciencia e a Tecnologia (FCT) SFRH/BPD/25661/2005; SFRH/BPD/63213/2009; SFRH/BPD/64905/2009; SFRH/BD/69785/2010; SFRH/BPD/47679/2008; PEst-C/CTM/LA0011/2013; SFRH/BPD/20833/2004; SFRH/BD/44410/2008; SFRH/BD/44474/2008; SFRH/BD/47450/2008; SFRH/BPD/47563/2008 / Fundação para a Ciência e a Tecnologia; Fundacao para a Ciencia e a Tecnologia (FCT) SOBREIRO/033, 035, 014, 034, 015, 017, 038, 019, 029, 039, 030, 036/2009 / National Consortium (COEC - Cork Oak ESTs Consortium)
Identifiants: 99136408709311
Unité académique: Centre d'Ecologie Fonctionnelle et Evolutive - CEFE
Langue: English
Type de ressource: Journal article