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

Autor: Maria Isabel Amorim, Rita Teresa Teixeira, Fernanda Simões, Teresa Ribeiro, Cândido Pinto Ricardo, Marília Horta, Miguel Pinheiro, Ana Isabel Rodrigues, Paulo Almeida, Tânia Almeida, Isabel Neves, Dora Batista, Maria Salomé Pais, Tatiana Santo, Ana Margarida Santos, Tiago Capote, Liliana Marum, Conceição Egas, Filomena Nóbrega, Maria João Gaspar, Sónia Gonçalves, Alfredo Cravador, Claudia S. Alabaça, Ana S. Fortunato, Isabel Carrasquinho, Nelson J. M. Saibo, José Graça, Teresa Lino-Neto, José B. Pereira-Leal, Mónica Sebastiana, Vera Inácio, Susana de Sousa Araújo, Aleix Badia, Andreia Miguel, Inês Chaves, Leonor Morais-Cecílio, José Carlos Rodrigues, Ana Margarida Fortes, José Leitão, Rómulo Sacramento Sobral, Andreas Bohn, Rui Manuel Tavares, Diogo Mendonça, Margarida Rocheta, José C. Matos, Carolina Varela, Rute Oliveira, Octávio S. Paulo, Maria Manuela Ribeiro Costa, Célia Miguel, Isabel A. Abreu, José C. Ramalho, Maria Helena Almeida, M. Margarida Oliveira, Jorge A. P. Paiva, Ana Ribeiro, Paula Sá-Pereira, Ana Coelho, João Raimundo, Maria Manuela Veloso, Rita Costa, Herlânder Azevedo, Carlos Faro
Přispěvatelé: Universidade do Minho
Rok vydání: 2014
Předmět:
Zdroj: BMC Genomics
Repositório Científico de Acesso Aberto de Portugal
Repositório Científico de Acesso Aberto de Portugal (RCAAP)
instacron:RCAAP
CIÊNCIAVITAE
ISSN: 1471-2164
DOI: 10.1186/1471-2164-15-371
Popis: 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 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.
This project was funded by "Fundacao para a Ciencia e a Tecnologia" (FCT) within a National Consortium (COEC - Cork Oak ESTs Consortium) that supported 12 sub-projects (SOBREIRO/033, 035, 014, 034, 015, 017, 038, 019, 029, 039, 030, 036/2009). The authors further wish to acknowledge FCT for ten doctoral (BD) and post doctoral (BPD) fellowships (Tania Almeida: SFRH/BD/44410/2008, Tiago Capote: SFRH/BD/69785/2010, Ines Chaves: SFRH/BPD/20833/2004, Ana S. Fortunato: SFRH/BPD/47563/2008, Marilia Horta: SFRH/BPD/63213/2009, Liliana Marum: "SFRH/BPD/47679/2008, Andreia Miguel: SFRH/BD/44474/2008, Margarida Rocheta: SFRH/BPD/64905/2009, Tatiana E. Santo: SFRH/BD/47450/2008, Monica Sebastiana: SFRH/BPD/25661/2005). Andreas Bohn, Nelson J.M. Saibo, Rita Teixeira were supported by the Programa Ciencia 2007, financed by POPH (QREN) and Isabel A. Abreu, Susana Araujo, Dora Batista, A. Margarida Fortes, Jorge A.P. Paiva, Sonia Goncalves by Programa Ciencia 2008, also funded by POPH (QREN). A Margarida Santos was funded through iBET (PEst-OE/EQB/LA0004/2011). Maintenance of the CorkOakDB is supported by the Instituto Gulbenkian de Ciencia.
Databáze: OpenAIRE
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