Physiology and Molecular Biology of Plants

, Volume 24, Issue 4, pp 535–549 | Cite as

Characterization of the cork formation and production transcriptome in Quercus cerris × suber hybrids

  • Brígida Meireles
  • Ana Usié
  • Pedro Barbosa
  • Ana Margarida Fortes
  • André Folgado
  • Inês Chaves
  • Isabel Carrasquinho
  • Rita Lourenço Costa
  • Sónia Gonçalves
  • Rita Teresa Teixeira
  • António Marcos Ramos
  • Filomena Nóbrega
Research Article


Cork oak is the main cork-producing species worldwide, and plays a significant economic, ecological and social role in the Mediterranean countries, in particular in Portugal and Spain. The ability to produce cork is limited to a few species, hence it must involve specific regulation mechanisms that are unique to these species. However, to date, these mechanisms remain largely understudied, especially with approaches involving the use of high-throughput sequencing technology. In this study, the transcriptome of cork-producing and non-cork-producing Quercus cerris × suber hybrids was analyzed in order to elucidate the differences between the two groups of trees displaying contrasting phenotypes for cork production. The results revealed the presence of a significant number of genes exclusively associated with cork production, in the trees that developed cork. Moreover, several gene ontology subcategories, such as cell wall biogenesis, lipid metabolic processes, metal ion binding and apoplast/cell wall, were only detected in the trees with cork production. These results indicate the existence, at the transcriptome level, of mechanisms that seem to be unique and necessary for cork production, which is an advancement in our knowledge regarding the genetic regulation behind cork formation and production.


Cork oak Transcriptome Cork production Hybrids 



This study was funded by Fundação para a Ciência e a Tecnologia (FCT) projects Cork Oak EST Consortium SOBREIRO/0017/2009 and UID/AGR/00115/2013. Financial support for AMR, AU and PB was provided by Investigador FCT project IF/00574/2012/CP1209/CT0001: “Genetic characterization of national animal and plant resources using next-generation sequencing”. Financial support for AMF was provided by projects PEst-OE/BIA/UI4046/2011 and FCT Investigator IF/00169/2015.

Author contribution

This study was conceived by IC, RC, AMF, RT, SG and FN (coordinator). Collection and identification of field material was performed by IC, RC and FN. Sample preparation and nucleic acid isolation were performed by RC and FN. qPCR validations were executed by AF and SG. Bioinformatics data analyses were conducted by BM, AU, PB, IC and AMR. Biological interpretation of the results was conducted by BM, AU, AMR, AMF, IC and FN. The manuscript was written by BM, AU, FN and AMR. All authors read and approved the final manuscript.

Data availability

Sequence reads were deposited in the NCBI Sequence Read Archive (SRA) under the accession numbers ERX143070 and ERX143071, for the normalized libraries, and SRX2677031 and SRX2677030, for the non-normalized libraries.

Compliance with ethical standards

Conflict of interest

The authors declare no conflict of interest.

Supplementary material

12298_2018_526_MOESM1_ESM.tif (170 kb)
Supplementary material 1 (TIFF 170 kb)
12298_2018_526_MOESM2_ESM.tif (118 kb)
Supplementary material 2 (TIFF 118 kb)
12298_2018_526_MOESM3_ESM.eps (466 kb)
Supplementary material 3 (EPS 465 kb)
12298_2018_526_MOESM4_ESM.eps (390 kb)
Supplementary material 4 (EPS 389 kb)
12298_2018_526_MOESM5_ESM.eps (428 kb)
Supplementary material 5 (EPS 427 kb)
12298_2018_526_MOESM6_ESM.xlsx (41 kb)
Supplementary material 6 (XLSX 40 kb)
12298_2018_526_MOESM7_ESM.xlsx (27 kb)
Supplementary material 7 (XLSX 27 kb)


  1. Alcázar R, Marco F, Cuevas JC et al (2006) Involvement of polyamines in plant response to abiotic stress. Biotechnol Lett 28:1867–1876. CrossRefPubMedGoogle Scholar
  2. Baxter HL, Stewart CN (2013) Effects of altered lignin biosynthesis on phenylpropanoid metabolism and plant stress. Biofuels 4:635–650. CrossRefGoogle Scholar
  3. Bugalho MN, Caldeira MC, Pereira JS et al (2011) Mediterranean cork oak savannas require human use to sustain biodiversity and ecosystem services. Front Ecol Environ 9:278–286. CrossRefGoogle Scholar
  4. Caritat A, Gutiérrez E, Molinas M (2000) Influence of weather on cork-ring width. Tree Physiol 20:893–900CrossRefPubMedGoogle Scholar
  5. Chevreux B, Pfisterer T, Drescher B et al (2004) Using the miraEST assembler for reliable and automated mRNA transcript assembly and SNP detection in sequenced ESTs. Genome Res 14:1147–1159CrossRefPubMedPubMedCentralGoogle Scholar
  6. Coberly LC, Rausher MD (2003) Analysis of a chalcone synthase mutant in Ipomoea purpurea reveals a novel function for flavonoids: amelioration of heat stress. Mol Ecol 12:1113–1124CrossRefPubMedGoogle Scholar
  7. Correia B, Valledor L, Meijón M et al (2013) Is the interplay between epigenetic markers related to the acclimation of cork oak plants to high temperatures ? PLoS ONE 8:e53543. CrossRefPubMedPubMedCentralGoogle Scholar
  8. Correia B, Rodriguez JL, Valledor L et al (2014) Analysis of the expression of putative heat-stress related genes in relation to thermotolerance of cork oak. J Plant Physiol 171:399–406. CrossRefPubMedGoogle Scholar
  9. Dao TTH, Linthorst HJM, Verpoorte R (2011) Chalcone synthase and its functions in plant resistance. Phytochem Rev 10:397–412. CrossRefPubMedPubMedCentralGoogle Scholar
  10. Denness L, McKenna JF, Segonzac C et al (2011) Cell wall damage-induced lignin biosynthesis is regulated by a reactive oxygen species- and jasmonic acid-dependent process in Arabidopsis. Plant Physiol 156:1364–1374. CrossRefPubMedPubMedCentralGoogle Scholar
  11. Ebadzad G, Cravador A (2014) Quantitative RT-PCR analysis of differentially expressed genes in Quercus suber in response to Phytophthora cinnamomi infection. SpringerPlus 3:613CrossRefPubMedPubMedCentralGoogle Scholar
  12. Ghouil H, Montpied P, Epron D et al (2003) Thermal optima of photosynthetic functions and thermostability of photochemistry in cork oak seedlings. Tree Physiol 23:1031–1040CrossRefPubMedGoogle Scholar
  13. Gollop R, Farhi S, Perl A (2001) Regulation of the leucoanthocyanidin dioxygenase gene expression in Vitis vinifera. Plant Sci 161:579–588CrossRefGoogle Scholar
  14. Graça J (2015) Suberin: the biopolyester at the frontier of plants. Front Chem. PubMedPubMedCentralCrossRefGoogle Scholar
  15. Graça J, Pereira H (2004) The periderm development in Quercus suber. IAWA J 25:325–335. CrossRefGoogle Scholar
  16. Graça J, Santos S (2007) Suberin: a biopolyester of plants’ skin. Macromol Biosci 7:128–135. CrossRefPubMedGoogle Scholar
  17. Grand C (1984) Ferulic acid 5-hydroxylase: a new cytochrome P-450-dependent enzyme from higher plant microsomes involved in lignin synthesis. FEBS Lett 169:7–11CrossRefGoogle Scholar
  18. Haas BJ, Papanicolaou A, Yassour M et al (2013) De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis. Nat Protoc 8:1494–1512. CrossRefPubMedGoogle Scholar
  19. Hu Z-L, Bao J, Reecy JM (2008) CateGOrizer: a web-based program to batch analyze gene on-tology classification categories. Online J Bioinform 9:108–112Google Scholar
  20. Huang B, Xu C (2008) Identification and characterization of proteins associated with plant tolerance to heat stress. J Integr Plant Biol 50:1230–1237. CrossRefPubMedGoogle Scholar
  21. Jones P, Binns D, Chang H-Y et al (2014) InterProScan 5: genome-scale protein function classification. Bioinformatics 30:1236–1240. CrossRefPubMedPubMedCentralGoogle Scholar
  22. Koes R, Verweij W, Quattrocchio F (2005) Flavonoids: a colorful model for the regulation and evolution of biochemical pathways. Trends Plant Sci 10:236–242. CrossRefPubMedGoogle Scholar
  23. Kolattukudy PE (1981) Structure, biosynthesis, and biodegradation of cutin and suberin. Annu Rev Plant Physiol 32:539–567. CrossRefGoogle Scholar
  24. Li H, Durbin R (2009) Fast and accurate short read alignment with Burrows–Wheeler transform. Bioinformatics 25:1754–1760. CrossRefPubMedPubMedCentralGoogle Scholar
  25. Li H, Handsaker B, Wysoker A et al (2009) The sequence alignment/map format and SAMtools. Bioinformatics 25:2078–2079. CrossRefPubMedPubMedCentralGoogle Scholar
  26. Lourenço A, Rencoret J, Chemetova C et al (2016) Lignin composition and structure differs between xylem, phloem and phellem in Quercus suber L. Front Plant Sci 10:10. CrossRefGoogle Scholar
  27. Maere S, Heymans K, Kuiper M (2005) BiNGO: a Cytoscape plugin to assess overrepresentation of Gene Ontology categories in Biological Networks. Bioinformatics 21:3448–3449. CrossRefPubMedGoogle Scholar
  28. Marques AV, Pereira H (2013) Lignin monomeric composition of corks from the barks of Betula pendula, Quercus suber and Quercus cerris determined by Py–GC–MS/FID. J Anal Appl Pyrolysis 100:88–94. CrossRefGoogle Scholar
  29. Marum L, Miguel A, Ricardo CP, Miguel C (2012) Reference gene selection for quantitative real-time PCR normalization in Quercus suber. PLoS ONE 7:e35113. CrossRefPubMedPubMedCentralGoogle Scholar
  30. McKenna A, Hanna M, Banks E et al (2010) The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res 20:1297–1303. CrossRefPubMedPubMedCentralGoogle Scholar
  31. Merico D, Isserlin R, Stueker O et al (2010) Enrichment map: a network-based method for gene-set enrichment visualization and interpretation. PLoS ONE 5:e13984. CrossRefPubMedPubMedCentralGoogle Scholar
  32. Miguel A, de Vega-Bartol J, Marum L et al (2015) Characterization of the cork oak transcriptome dynamics during acorn development. BMC Plant Biol. PubMedPubMedCentralCrossRefGoogle Scholar
  33. Mizrachi E, Mansfield SD, Myburg AA (2012) Cellulose factories: advancing bioenergy production from forest trees. New Phytol 194:54–62. CrossRefPubMedGoogle Scholar
  34. Park YB, Cosgrove DJ (2015) Xyloglucan and its interactions with other components of the growing cell wall. Plant Cell Physiol 56:180–194. CrossRefPubMedGoogle Scholar
  35. Pereira H (1988) Chemical composition and variability of cork from Quercus suber. Wood Sci Technol 22:211–218CrossRefGoogle Scholar
  36. Pereira H (2007) Cork: biology, production and uses, 1st edn. Elsevier, LondonGoogle Scholar
  37. Pereira-Leal JB, Abreu IA, Alabaça CS et al (2014) A comprehensive assessment of the transcriptome of cork oak (Quercus suber) through EST sequencing. BMC Genom 15:371CrossRefGoogle Scholar
  38. Pfaffl M (2001) A new mathematical model for relative quantification in real-time RT-PCR. Nucleic Acids Res 29:e45CrossRefPubMedPubMedCentralGoogle Scholar
  39. Pla M, Huguet G, Verdaguer D et al (1998) Stress proteins co-expressed in suberized and lignified cells and in apical meristems. Plant Sci 139:49–57CrossRefGoogle Scholar
  40. Pollard M, Beisson F, Li Y, Ohlrogge JB (2008) Building lipid barriers: biosynthesis of cutin and suberin. Trends Plant Sci 13:236–246. CrossRefPubMedGoogle Scholar
  41. Rahantamalala A, Rech P, Martinez Y et al (2010) Research article coordinated transcriptional regulation of two key genes in the lignin branch pathway-CAD and CCR-is mediated through MYB-binding sites. BMC Plant Biol 10(1):130CrossRefPubMedPubMedCentralGoogle Scholar
  42. Ranathunge K, Schreiber L, Franke R (2011) Suberin research in the genomics era—new interest for an old polymer. Plant Sci 180:399–413. CrossRefPubMedGoogle Scholar
  43. Ravanel S, Block MA, Rippert P et al (2004) Methionine metabolism in plants: chloroplasts are autonomous for de novo methionine synthesis and can import S-adenosylmethionine from the cytosol. J Biol Chem 279:22548–22557. CrossRefPubMedGoogle Scholar
  44. Reid KE, Olsson N, Schlosser J et al (2006) An optimized grapevine RNA isolation procedure and statistical determination of reference genes for real-time RT-PCR during berry development. BMC Plant Biol 6:27CrossRefPubMedPubMedCentralGoogle Scholar
  45. Ricardo CPP, Martins I, Francisco R et al (2011) Proteins associated with cork formation in Quercus suber L. stem tissues. J Proteomics 74:1266–1278. CrossRefPubMedGoogle Scholar
  46. Robinson MD, McCarthy DJ, Smyth GK (2010) edgeR: a bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics 26:139–140. CrossRefPubMedPubMedCentralGoogle Scholar
  47. Schloss PD, Westcott SL, Ryabin T et al (2009) Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol 75:7537–7541. CrossRefPubMedPubMedCentralGoogle Scholar
  48. Serra O, Soler M, Hohn C et al (2009) CYP86A33-targeted gene silencing in potato tuber alters suberin composition, distorts suberin lamellae, and impairs the periderm’s water barrier function. Plant Physiol 149:1050–1060. CrossRefPubMedPubMedCentralGoogle Scholar
  49. Serra O, Figueras M, Franke R et al (2010) Unraveling ferulate role in suberin and periderm biology by reverse genetics. Plant Signal Behav 5:953–958CrossRefPubMedPubMedCentralGoogle Scholar
  50. Shannon P, Markiel A, Ozier O et al (2003) Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res 13:2498–2504CrossRefPubMedPubMedCentralGoogle Scholar
  51. Silva SP, Sabino MA, Fernandes EM et al (2005) Cork: properties, capabilities and applications. Int Mater Rev 50:256. CrossRefGoogle Scholar
  52. Soler M, Serra O, Molinas M et al (2007) A genomic approach to suberin biosynthesis and cork differentiation. Plant Physiol 144:419–431. CrossRefPubMedPubMedCentralGoogle Scholar
  53. Srivastava AC, Dasgupta K, Ajieren E et al (2009) Arabidopsis plants harbouring a mutation in AtSUC2, encoding the predominant sucrose/proton symporter necessary for efficient phloem transport, are able to complete their life cycle and produce viable seed. Ann Bot 104:1121–1128. CrossRefPubMedPubMedCentralGoogle Scholar
  54. Sturm A (1999) Invertases. Primary structures, functions, and roles in plant development and sucrose partitioning. Plant Physiol 121:1–8CrossRefPubMedPubMedCentralGoogle Scholar
  55. Teixeira RT, Fortes AM, Pinheiro C, Pereira H (2014) Comparison of good- and bad-quality cork: application of high-throughput sequencing of phellogenic tissue. J Exp Bot 65:4887–4905. CrossRefPubMedGoogle Scholar
  56. Untergasser A, Nijveen H, Rao X, Bisseling T, Geurts R, Leunissen JA (2007) Primer3Plus, an enhanced web interface to Primer3. Nucleic Acids Res 35(suppl_2):W71–W74CrossRefPubMedPubMedCentralGoogle Scholar
  57. Verdaguer R, Soler M, Serra O et al (2016) Silencing of the potato StNAC103 gene enhances the accumulation of suberin polyester and associated wax in tuber skin. J Exp Bot 67:5415–5427. CrossRefPubMedPubMedCentralGoogle Scholar
  58. Vishwanath SJ, Delude C, Domergue F, Rowland O (2015) Suberin: biosynthesis, regulation, and polymer assembly of a protective extracellular barrier. Plant Cell Rep 34:573–586. CrossRefPubMedGoogle Scholar
  59. Wang H, Ng TB (2002) Isolation of an antifungal thaumatin-like protein from kiwi fruits. Phytochemistry 61:1–6CrossRefPubMedGoogle Scholar
  60. Wang W, Vinocur B, Shoseyov O, Altman A (2004) Role of plant heat-shock proteins and molecular chaperones in the abiotic stress response. Trends Plant Sci 9:244–252. CrossRefPubMedGoogle Scholar
  61. Zhu YY, Machleder EM, Chenchik A et al (2001) Reverse transcriptase template switching: a SMART™ approach for full-length cDNA library construction. Biotechniques 30:892–897PubMedCrossRefGoogle Scholar
  62. Zhulidov PA, Bogdanova EA, Shcheglov AS et al (2005) A method for the preparation of normalized cDNA libraries enriched with full-length sequences. Russ J Bioorganic Chem 31:170–177CrossRefGoogle Scholar

Copyright information

© Prof. H.S. Srivastava Foundation for Science and Society 2018

Authors and Affiliations

  • Brígida Meireles
    • 1
  • Ana Usié
    • 1
    • 2
  • Pedro Barbosa
    • 1
  • Ana Margarida Fortes
    • 3
  • André Folgado
    • 1
  • Inês Chaves
    • 1
  • Isabel Carrasquinho
    • 4
  • Rita Lourenço Costa
    • 4
    • 5
  • Sónia Gonçalves
    • 1
    • 7
  • Rita Teresa Teixeira
    • 6
  • António Marcos Ramos
    • 1
    • 2
  • Filomena Nóbrega
    • 4
  1. 1.Centro de Biotecnologia Agrícola e Agro-Alimentar do Alentejo (CEBAL)Instituto Politécnico de Beja (IPBeja)BejaPortugal
  2. 2.Instituto de Ciências Agrárias e Ambientais Mediterrânicas (ICAAM)Universidade de ÉvoraÉvoraPortugal
  3. 3.Faculdade de Ciências de Lisboa, Biosystems and Integrative Sciences Institute (BIOISI)Universidade de LisboaLisbonPortugal
  4. 4.Instituto Nacional de Investigação Agrária e Veterinária, I.P, Quinta do MarquêsOeirasPortugal
  5. 5.Centro de estudos Florestais, Instituto Superior de AgronomiaUniversidade de LisboaLisbonPortugal
  6. 6.Instituto Superior de Agronomia da Universidade de Lisboa (ISA)LisbonPortugal
  7. 7.Wellcome Trust Sanger InstituteCambridgeUK

Personalised recommendations