Please login first
Quercus suber transcriptome analyses: identification of genes and SNPs related to cork quality
1 , * 1, 2 , 1, 3 , 1, 4 , 1, 5 , 1, 2 , 1, 6 , 1, 2
1  CEBAL - Centro de Biotecnologia Agrícola e Agro-Alimentar do Alentejo / IPBeja - Instituto Politécnico de Beja, 7801-908 Beja, Portugal
2  MED-Mediterranean Institute for Agriculture, Environment and Development, Évora, Portugal
3  Center for Genomics and Systems Biology, New York University Abu Dhabi, Saadiyat Island, Abu Dhabi, United Arab Emirates
4  GenoMed – Diagnósticos de Medicina Molecular SA. Edificio Egas Moniz, Av. Prof. Egas Moniz, 1649-028 Lisboa, Portugal.
5  CICECO – Aveiro Institute of Materials, Department of Chemistry, University of Aveiro, 3810-193 Aveiro, Portugal
6  Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, CB10 1SA, UK
Academic Editor: Iker Aranjuelo


Cork is an ancestral natural material derived from the cork oak tree, with multiple industrial applications [1]. The cork quality, one of the main concerns of cork industry, strongly influences the market value of this non-wood product, which plays an important role in the Mediterranean economies. It is known that cork quality is dependent on both genetic and environmental factors. The recent sequencing of the cork oak genome allowed a very comprehensive characterization of the species’ genome and opened the possibility to execute numerous studies to appraise old and new questions that cork production continues to raise [2].

In this study, the transcriptome of phellogen tissue harvested from cork oak trees producing good and bad quality cork was performed using Illumina sequencing data in order to elucidate differentially expressed genes (DEGs), gene ontology (GO), and functional pathway analysis. Additionally, a variant calling analyses was performed in order to identify differences between trees from each group.

The results revealed the presence of highly-expressed genes involved in stress response, transmembrane transport and proteolysis, in trees producing cork of bad quality. On the other hand, genes involved in the fatty acid biosynthetic pathway, resulting in important precursors of waxes and some suberin monomers, were highly expressed in trees producing good quality cork. A total of 296,640 variants were identified of which 159,248 were high-quality Single Nucleotide Polymorphisms (SNPs).

This study highlights a set of mechanisms that the trees activate during cork differentiation, and which can influence the cork quality.


[1] Duarte AP and Bordado JC (2015) Cork – a renewable raw material: forecast of industrial potential and development priorities. doi: 10.3389/fmats.2015.00002

[2] Ramos AM, Usié A, Barbosa P, Barros PM, Capote T, Chaves I, Simões F, Abreu I, Carrasquinho I, Faro C, et al (2018) The draft genome sequence of cork oak. Sci data 5: 180069

Acknowledgements: Work was supported by InAlentejo under the scope “GenoSuber - Cork oak genome sequencing” (ALENT-07-0224-FEDER-001754) and by Alentejo2020, through FEDER under the scope “Lentidev - A genomic approach to cork quality” (ALT20-03-0145-FEDER-000020). Authors also acknowledge FCT for Contrato – Programa to L. Marum (CEECINST/00131/2018) and FCT for UIDB/05183/2020.

Keywords: Quercus suber; transcriptome; cork quality; RNA-Seq;