title: Characterization of the cork oak transcriptome dynamics during acorn development.
abstract: BACKGROUND
  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.
authors.affiliation: Instituto de Biologia Experimental e Tecnológica, Apartado 12, 2781-901, Oeiras, Portugal. andreiamiguel@itqb.unl.pt.|Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Avenida da República, 2780-157, Oeiras, Portugal. andreiamiguel@itqb.unl.pt.
authors.forename: Andreia
authors.initials: A
authors.lastname: Miguel
authors.affiliation: Instituto de Biologia Experimental e Tecnológica, Apartado 12, 2781-901, Oeiras, Portugal. devegabartol@itqb.unl.pt.|Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Avenida da República, 2780-157, Oeiras, Portugal. devegabartol@itqb.unl.pt.|The Genome Analysis Centre, Norwich Research Park, Norwich, NR4 7UH, UK. devegabartol@itqb.unl.pt.
authors.forename: José
authors.initials: J
authors.lastname: de Vega-Bartol
authors.affiliation: Instituto de Biologia Experimental e Tecnológica, Apartado 12, 2781-901, Oeiras, Portugal. marum@itqb.unl.pt.|Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Avenida da República, 2780-157, Oeiras, Portugal. marum@itqb.unl.pt.|KLÓN, Innovative Technologies from Cloning, Biocant Park, Núcleo 4, Lote 4A, 3060-197, Cantanhede, Portugal. marum@itqb.unl.pt.
authors.forename: Liliana
authors.initials: L
authors.lastname: Marum
authors.affiliation: Instituto de Biologia Experimental e Tecnológica, Apartado 12, 2781-901, Oeiras, Portugal. ichaves@itqb.unl.pt.|Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Avenida da República, 2780-157, Oeiras, Portugal. ichaves@itqb.unl.pt.
authors.forename: Inês
authors.initials: I
authors.lastname: Chaves
authors.affiliation: Laboratory of Genomics and Genetic Improvement, BioFIG, FCT, Universidade do Algarve, E.8, Campus de Gambelas, Faro, 8300, Portugal. ts.tatianasanto@gmail.com.
authors.forename: Tatiana
authors.initials: T
authors.lastname: Santo
authors.affiliation: Laboratory of Genomics and Genetic Improvement, BioFIG, FCT, Universidade do Algarve, E.8, Campus de Gambelas, Faro, 8300, Portugal. jleitao@ualg.pt.
authors.forename: José
authors.initials: J
authors.lastname: Leitão
authors.affiliation: INIAV- Instituto Nacional de Investigação Agrária e Veterinária, IP, Quinta do, Marquês, Oeiras, 2780-159, Portugal. carolina.varela@iniav.pt.
authors.forename: Maria Carolina
authors.initials: MC
authors.lastname: Varela
authors.affiliation: Instituto de Biologia Experimental e Tecnológica, Apartado 12, 2781-901, Oeiras, Portugal. cmiguel@itqb.unl.pt.|Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Avenida da República, 2780-157, Oeiras, Portugal. cmiguel@itqb.unl.pt.
authors.forename: Célia M
authors.initials: CM
authors.lastname: Miguel
mesh_terms: D001692:Biological Transport / Q000235:genetics; D016000:Cluster Analysis; D020869:Gene Expression Profiling; D018507:Gene Expression Regulation, Developmental; D018506:Gene Expression Regulation, Plant; D015723:Gene Library; D058977:Molecular Sequence Annotation; D029963:Quercus / Q000196:embryology* / Q000235:genetics*; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism; D060888:Real-Time Polymerase Chain Reaction; D015203:Reproducibility of Results; D012639:Seeds / Q000196:embryology* / Q000235:genetics*; D017423:Sequence Analysis, RNA; D015398:Signal Transduction / Q000235:genetics; D059467:Transcriptome / Q000235:genetics*; D014867:Water
chemical_list: D012333:RNA, Messenger; D014867:Water