title: A comprehensive assessment of the transcriptome of cork oak (Quercus suber) through EST sequencing.
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.
  
  
  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.
authors.affiliation: Instituto Gulbenkian de Ciência, Rua da Quinta Grande 6, Oeiras 2780-156, Portugal. jleal@igc.gulbenkian.pt.
authors.forename: José B
authors.initials: JB
authors.lastname: Pereira-Leal
authors.forename: Isabel A
authors.initials: IA
authors.lastname: Abreu
authors.forename: Cláudia S
authors.initials: CS
authors.lastname: Alabaça
authors.forename: Maria Helena
authors.initials: MH
authors.lastname: Almeida
authors.forename: Paulo
authors.initials: P
authors.lastname: Almeida
authors.forename: Tânia
authors.initials: T
authors.lastname: Almeida
authors.forename: Maria Isabel
authors.initials: MI
authors.lastname: Amorim
authors.forename: Susana
authors.initials: S
authors.lastname: Araújo
authors.forename: Herlânder
authors.initials: H
authors.lastname: Azevedo
authors.forename: Aleix
authors.initials: A
authors.lastname: Badia
authors.forename: Dora
authors.initials: D
authors.lastname: Batista
authors.forename: Andreas
authors.initials: A
authors.lastname: Bohn
authors.forename: Tiago
authors.initials: T
authors.lastname: Capote
authors.forename: Isabel
authors.initials: I
authors.lastname: Carrasquinho
authors.forename: Inês
authors.initials: I
authors.lastname: Chaves
authors.forename: Ana Cristina
authors.initials: AC
authors.lastname: Coelho
authors.forename: Maria Manuela Ribeiro
authors.initials: MM
authors.lastname: Costa
authors.forename: Rita
authors.initials: R
authors.lastname: Costa
authors.forename: Alfredo
authors.initials: A
authors.lastname: Cravador
authors.forename: Conceição
authors.initials: C
authors.lastname: Egas
authors.forename: Carlos
authors.initials: C
authors.lastname: Faro
authors.forename: Ana M
authors.initials: AM
authors.lastname: Fortes
authors.forename: Ana S
authors.initials: AS
authors.lastname: Fortunato
authors.forename: Maria João
authors.initials: MJ
authors.lastname: Gaspar
authors.forename: Sónia
authors.initials: S
authors.lastname: Gonçalves
authors.forename: José
authors.initials: J
authors.lastname: Graça
authors.forename: Marília
authors.initials: M
authors.lastname: Horta
authors.forename: Vera
authors.initials: V
authors.lastname: Inácio
authors.forename: José M
authors.initials: JM
authors.lastname: Leitão
authors.forename: Teresa
authors.initials: T
authors.lastname: Lino-Neto
authors.forename: Liliana
authors.initials: L
authors.lastname: Marum
authors.forename: José
authors.initials: J
authors.lastname: Matos
authors.forename: Diogo
authors.initials: D
authors.lastname: Mendonça
authors.forename: Andreia
authors.initials: A
authors.lastname: Miguel
authors.forename: Célia M
authors.initials: CM
authors.lastname: Miguel
authors.forename: Leonor
authors.initials: L
authors.lastname: Morais-Cecílio
authors.forename: Isabel
authors.initials: I
authors.lastname: Neves
authors.forename: Filomena
authors.initials: F
authors.lastname: Nóbrega
authors.forename: Maria Margarida
authors.initials: MM
authors.lastname: Oliveira
authors.forename: Rute
authors.initials: R
authors.lastname: Oliveira
authors.forename: Maria Salomé
authors.initials: MS
authors.lastname: Pais
authors.forename: Jorge A
authors.initials: JA
authors.lastname: Paiva
authors.forename: Octávio S
authors.initials: OS
authors.lastname: Paulo
authors.forename: Miguel
authors.initials: M
authors.lastname: Pinheiro
authors.forename: João A P
authors.initials: JA
authors.lastname: Raimundo
authors.forename: José C
authors.initials: JC
authors.lastname: Ramalho
authors.forename: Ana I
authors.initials: AI
authors.lastname: Ribeiro
authors.forename: Teresa
authors.initials: T
authors.lastname: Ribeiro
authors.forename: Margarida
authors.initials: M
authors.lastname: Rocheta
authors.forename: Ana Isabel
authors.initials: AI
authors.lastname: Rodrigues
authors.forename: José C
authors.initials: JC
authors.lastname: Rodrigues
authors.forename: Nelson J M
authors.initials: NJ
authors.lastname: Saibo
authors.forename: Tatiana E
authors.initials: TE
authors.lastname: Santo
authors.forename: Ana Margarida
authors.initials: AM
authors.lastname: Santos
authors.forename: Paula
authors.initials: P
authors.lastname: Sá-Pereira
authors.forename: Mónica
authors.initials: M
authors.lastname: Sebastiana
authors.forename: Fernanda
authors.initials: F
authors.lastname: Simões
authors.forename: Rómulo S
authors.initials: RS
authors.lastname: Sobral
authors.forename: Rui
authors.initials: R
authors.lastname: Tavares
authors.forename: Rita
authors.initials: R
authors.lastname: Teixeira
authors.forename: Carolina
authors.initials: C
authors.lastname: Varela
authors.forename: Maria Manuela
authors.initials: MM
authors.lastname: Veloso
authors.forename: Cândido P P
authors.initials: CP
authors.lastname: Ricardo
mesh_terms: D018744:DNA, Plant / Q000032:analysis; D020224:Expressed Sequence Tags; D015723:Gene Library; D010802:Phylogeny; D029963:Quercus / Q000235:genetics* / Q000254:growth & development; D017422:Sequence Analysis, DNA; D059467:Transcriptome
chemical_list: D018744:DNA, Plant