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

2014-05-15Journal article Open access
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dc.contributor.authorPereira-Leal, José B.
dc.contributor.authorAbreu, Isabel A.
dc.contributor.authorAlabaça, Cláudia S.
dc.contributor.authorAlmeida, Maria H.
dc.contributor.authorAlmeida, Paulo
dc.contributor.authorAlmeida, Tânia
dc.contributor.authorAmorim, Maria I.
dc.contributor.authorAraújo, Susana
dc.contributor.authorAzevedo, Herlânder
dc.contributor.authorBadia, Aleix
dc.contributor.authorBatista, Dora
dc.contributor.authorBohn, Andreas
dc.contributor.authorCapote, Tiago
dc.contributor.authorCarrasquinho, Isabel
dc.contributor.authorChaves, Inês
dc.contributor.authorCoelho, A. C.
dc.contributor.authorCosta, Maria M. R.
dc.contributor.authorCosta, Rita
dc.contributor.authorCravador, A.
dc.contributor.authorEgas, Conceição
dc.contributor.authorFaro, Carlos
dc.contributor.authorFortes, Ana M.
dc.contributor.authorFortunato, Ana S.
dc.contributor.authorGaspar, Maria J.
dc.contributor.authorGonçalves, Sónia
dc.contributor.authorGraça, José
dc.contributor.authorHorta, Marília
dc.contributor.authorInácio, Vera
dc.contributor.authorLeitão, J. M.
dc.contributor.authorLino-Neto, Teresa
dc.contributor.authorMarum, Liliana
dc.contributor.authorMatos, José
dc.contributor.authorMendonça, Diogo
dc.contributor.authorMiguel, Andreia
dc.contributor.authorMiguel, Célia M.
dc.contributor.authorMorais-Cecílio, Leonor
dc.contributor.authorNeves, Isabel
dc.contributor.authorNóbrega, Filomena
dc.contributor.authorOliveira, Maria M.
dc.contributor.authorOliveira, Rute
dc.contributor.authorPais, Maria S.
dc.contributor.authorPaiva, Jorge A.
dc.contributor.authorPaulo, O. S.
dc.contributor.authorPinheiro, Miguel
dc.contributor.authorRaimundo, João A. P.
dc.contributor.authorRamalho, J. C.
dc.contributor.authorRibeiro, Ana I.
dc.contributor.authorRibeiro, Teresa
dc.contributor.authorRocheta, Margarida
dc.contributor.authorRodrigues, Ana I.
dc.contributor.authorRodrigues, José C.
dc.contributor.authorSaibo, Nelson J. M.
dc.contributor.authorSanto, Tatiana
dc.contributor.authorSantos, Ana M.
dc.contributor.authorSá-Pereira, Paula
dc.contributor.authorSebastiana, Mónica
dc.contributor.authorSimões, Fernanda
dc.contributor.authorSobral, Rómulo S.
dc.contributor.authorTavares, Rui
dc.contributor.authorTeixeira, Rita
dc.contributor.authorVarela, Carolina
dc.contributor.authorVeloso, Maria M.
dc.contributor.authorRicardo, Cândido P. P.
dc.date.accessioned2014-06-24T12:07:56Z
dc.date.available2014-06-24T12:07:56Z
dc.date.issued2014-05-15
dc.date.updated2014-06-18T11:04:14Z
dc.description.abstractBackground: 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.por
dc.description.versioninfo:eu-repo/semantics/publishedVersion
dc.identifier.citationBMC Genomics. 2014 May 15;15(1):371por
dc.identifier.doihttp://dx.doi.org/10.1186/1471-2164-15-371
dc.identifier.urihttp://hdl.handle.net/10400.1/4471
dc.language.isoengpor
dc.peerreviewedyespor
dc.publisherBioMed Centralpor
dc.relationMOLECULAR REGULATION OF CORK DEVELOPMENT - THE ROLE OF THE TRANSCRIPTION FACTOR QSR2R3MYB
dc.relationGENES THAT CONTROL SEX DETERMINATION AND EVOLUTION OF MONOEICY IN GRAPEVINE: THE ROLE OF FLOWER MERISTEM AND ORGAN IDENTITY GENES
dc.relationIMPACT OF DROUGHT ON THE PHOTOSYNTHETIC APPARATUS OF COFFEA SPP.: AN INTEGRATIVE APPROACH
dc.relationMOLECULAR MECHANISMS OF THE ROGUE PARAMUTATION IN PISUM SATIVUM L.
dc.relationMOLECULAR REGULATION OF SECONDARY GROWTH: SEARCHING FOR SHORT-ROOT FUNCTION IN CORK FORMATION
dc.rights.urihttp://creativecommons.org/licenses/by/2.0
dc.titleA comprehensive assessment of the transcriptome of cork oak (Quercus suber) through EST sequencingpor
dc.typejournal article
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oaire.awardTitleMOLECULAR REGULATION OF CORK DEVELOPMENT - THE ROLE OF THE TRANSCRIPTION FACTOR QSR2R3MYB
oaire.awardTitleGENES THAT CONTROL SEX DETERMINATION AND EVOLUTION OF MONOEICY IN GRAPEVINE: THE ROLE OF FLOWER MERISTEM AND ORGAN IDENTITY GENES
oaire.awardTitleIMPACT OF DROUGHT ON THE PHOTOSYNTHETIC APPARATUS OF COFFEA SPP.: AN INTEGRATIVE APPROACH
oaire.awardTitleMOLECULAR MECHANISMS OF THE ROGUE PARAMUTATION IN PISUM SATIVUM L.
oaire.awardTitleMOLECULAR REGULATION OF SECONDARY GROWTH: SEARCHING FOR SHORT-ROOT FUNCTION IN CORK FORMATION
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oaire.citation.endPage14por
oaire.citation.issue1:371por
oaire.citation.startPage1por
oaire.citation.titleBMC Genomicspor
oaire.citation.volume15por
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