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 is a preview of subscription content, log in to check access.
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.
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.
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.
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
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
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
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
Gollop R, Farhi S, Perl A (2001) Regulation of the leucoanthocyanidin dioxygenase gene expression in Vitis vinifera. Plant Sci 161:579–588CrossRefGoogle Scholar
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
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
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
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
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