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Characterization of the cork oak transcriptome dynamics during acorn development

2015-06-25Journal article Open Access
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dc.contributor.authorMiguel, Andreia
dc.contributor.authorde Vega-Bartol, José
dc.contributor.authorMarum, Liliana
dc.contributor.authorChaves, Inês
dc.contributor.authorSanto, Tatiana
dc.contributor.authorLeitão, J. M.
dc.contributor.authorVarela, Maria C.
dc.contributor.authorMiguel, Célia M.
dc.date.accessioned2015-09-08T11:15:58Z
dc.date.available2015-09-08T11:15:58Z
dc.date.issued2015-06-25
dc.date.updated2015-08-03T15:57:13Z
dc.description.abstractBackground: Cork oak (Quercus suber L.) has a natural distribution across western Mediterranean regions and is a keystone forest tree species in these ecosystems. The fruiting phase is especially critical for its regeneration but the molecular mechanisms underlying the biochemical and physiological changes during cork oak acorn development are poorly understood. In this study, the transcriptome of the cork oak acorn, including the seed, was characterized in five stages of development, from early development to acorn maturation, to identify the dominant processes in each stage and reveal transcripts with important functions in gene expression regulation and response to water. Results: A total of 80,357 expressed sequence tags (ESTs) were de novo assembled from RNA-Seq libraries representative of the several acorn developmental stages. Approximately 7.6 % of the total number of transcripts present in Q. suber transcriptome was identified as acorn specific. The analysis of expression profiles during development returned 2,285 differentially expressed (DE) transcripts, which were clustered into six groups. The stage of development corresponding to the mature acorn exhibited an expression profile markedly different from other stages. Approximately 22 % of the DE transcripts putatively code for transcription factors (TF) or transcriptional regulators, and were found almost equally distributed among the several expression profile clusters, highlighting their major roles in controlling the whole developmental process. On the other hand, carbohydrate metabolism, the biological pathway most represented during acorn development, was especially prevalent in mid to late stages as evidenced by enrichment analysis. We further show that genes related to response to water, water deprivation and transport were mostly represented during the early (S2) and the last stage (S8) of acorn development, when tolerance to water desiccation is possibly critical for acorn viability. Conclusions: To our knowledge this work represents the first report of acorn development transcriptomics in oaks. The obtained results provide novel insights into the developmental biology of cork oak acorns, highlighting transcripts putatively involved in the regulation of the gene expression program and in specific processes likely essential for adaptation. It is expected that this knowledge can be transferred to other oak species of great ecological value.por
dc.description.sponsorshipFundação para a Ciência e a Tecnologiapor
dc.identifier.citationBMC Plant Biology. 2015 Jun 25;15(1):158por
dc.identifier.doihttp://dx.doi.org/10.1186/s12870-015-0534-1
dc.identifier.urihttp://hdl.handle.net/10400.1/6743
dc.language.isoengpor
dc.peerreviewedyespor
dc.publisherBioMed Centralpor
dc.relationStrategic Project - LA 4 - 2011-2012
dc.relationBioresources 4 Sustainability
dc.rights.holderMiguel et al.
dc.subjectQuercus suberpor
dc.subjectCarbohydrate metabolismpor
dc.subjectFruitpor
dc.subjectSeedpor
dc.subjectTranscriptomicspor
dc.subjectTranscription factorpor
dc.subjectTranscriptional regulatorspor
dc.subjectResponse to waterpor
dc.titleCharacterization of the cork oak transcriptome dynamics during acorn developmentpor
dc.typejournal article
dspace.entity.typePublication
oaire.awardTitleStrategic Project - LA 4 - 2011-2012
oaire.awardTitleBioresources 4 Sustainability
oaire.awardURIinfo:eu-repo/grantAgreement/FCT/6817 - DCRRNI ID/PEst-OE%2FEQB%2FLA0004%2F2011/PT
oaire.awardURIinfo:eu-repo/grantAgreement/FCT/6817 - DCRRNI ID/UID%2FMulti%2F04551%2F2013/PT
oaire.awardURIinfo:eu-repo/grantAgreement/FCT/3599-PPCDT/SOBREIRO%2F0029%2F2009/PT
oaire.awardURIinfo:eu-repo/grantAgreement/FCT/Investigador FCT/IF%2F01168%2F2013%2FCP1176%2FCT0001/PT
oaire.citation.issue(1):158por
oaire.citation.titleBMC Plant Biologypor
oaire.citation.volume15por
oaire.fundingStream6817 - DCRRNI ID
oaire.fundingStream6817 - DCRRNI ID
oaire.fundingStream3599-PPCDT
oaire.fundingStreamInvestigador FCT
person.familyNameLeitão
person.givenNameJosé
person.identifier258398
person.identifier.ciencia-id7A17-3E0A-73AD
person.identifier.orcid0000-0003-4278-0415
person.identifier.ridAAH-3958-2020
person.identifier.scopus-author-id7005119796
project.funder.identifierhttp://doi.org/10.13039/501100001871
project.funder.identifierhttp://doi.org/10.13039/501100001871
project.funder.identifierhttp://doi.org/10.13039/501100001871
project.funder.identifierhttp://doi.org/10.13039/501100001871
project.funder.nameFundação para a Ciência e a Tecnologia
project.funder.nameFundação para a Ciência e a Tecnologia
project.funder.nameFundação para a Ciência e a Tecnologia
project.funder.nameFundação para a Ciência e a Tecnologia
rcaap.rightsopenAccesspor
rcaap.typearticlepor
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