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

Publication . Pereira-Leal, José B.; Abreu, Isabel A.; Alabaça, Cláudia S.; Almeida, Maria H.; Almeida, Paulo; Almeida, Tânia; Amorim, Maria I.; Araújo, Susana; Azevedo, Herlânder; Badia, Aleix; Batista, Dora; Bohn, Andreas; Capote, Tiago; Carrasquinho, Isabel; Chaves, Inês; Coelho, A. C.; Costa, Maria M. R.; Costa, Rita; Cravador, A.; Egas, Conceição; Faro, Carlos; Fortes, Ana M.; Fortunato, Ana S.; Gaspar, Maria J.; Gonçalves, Sónia; Graça, José; Horta, Marília; Inácio, Vera; Leitão, J. M.; Lino-Neto, Teresa; Marum, Liliana; Matos, José; Mendonça, Diogo; Miguel, Andreia; Miguel, Célia M.; Morais-Cecílio, Leonor; Neves, Isabel; Nóbrega, Filomena; Oliveira, Maria M.; Oliveira, Rute; Pais, Maria S.; Paiva, Jorge A.; Paulo, O. S.; Pinheiro, Miguel; Raimundo, João A. P.; Ramalho, J. C.; Ribeiro, Ana I.; Ribeiro, Teresa; Rocheta, Margarida; Rodrigues, Ana I.; Rodrigues, José C.; Saibo, Nelson J. M.; Santo, Tatiana; Santos, Ana M.; Sá-Pereira, Paula; Sebastiana, Mónica; Simões, Fernanda; Sobral, Rómulo S.; Tavares, Rui; Teixeira, Rita; Varela, Carolina; Veloso, Maria M.; Ricardo, Cândido P. P.

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. 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.

2014-05-15Journal article

Open access

Quercus suber – P. cinnamomi interaction: hypothetical molecular mechanism model

Publication . Coelho, A. C.; Horta, Marília; Ebadzad, G.; Cravador, A.

Phytophthora cinnamomi Rands is involved in the decline and mortality of Quercus suber L. and Quercus ilex L. in Southern Europe, in particular in Portugal and Spain. The presence and spread of P. cinnamomi in these regions is a severe threat to these oak ecosystems leading to expectable severe consequences for the production of cork and acorns in the near future. Molecular mechanisms underlying oomycete-host interactions are poorly understood. As a first step to identify transcripts involved in the Quercus suber – Phytophthora cinnamomi interaction, we applied complementary deoxyribonucleic acidamplified fragment length polymorphism (cDNA-AFLP) methodology to cork oak seedlings infected with zoospores or mycelium of P. cinnamomi. Forty-four Quercus suber genes that were differentially expressed when exposed to Phytophthora cinnamomi were selected and sequenced. Several of these genes were fully sequenced and the deduced aminoacid sequences showed consistent homology with proteins involved in the defence mechanism of other plant species. These findings led to the design of a simplified hypothetical model that illustrates the initial events of the interaction between Q. suber and P. cinnamomi.

2011Journal article

Open access