Gene co-expression analysis identifies candidate epigenetic regulatory modules of periderm development

The periderm, a protective tissue formed during secondary growth, acts as a defence barrier against environmental stress. In cork oak (Quercus suber L.), a long-lived phellogen (cork cambium) generates a thick, suberized cork layer with significant ecological and economic value. While epigenetic regulation of periderm development has been suggested (reviewed in Inácio et al., 2022), the underlying genetic components remain largely uncharacterized. Here, we identify candidate epigenetic regulatory modules of periderm development in Quercus suber through a targeted co-expression analysis of 89 publicly available RNA-seq libraries, primarily from stem and root tissues. Normalized raw read counts were used to compute gene co-expression, focusing on 134 epigenetic regulators associated with DNA methylation/demethylation, histone modifications, and chromatin remodelling. Co-expression analysis was conducted applying 12 correlation methods, and a final network resulting from the aggregation of all correlation methods was obtained, representing selected epigenetic markers with strong co-expression with 3219 candidate target genes. Histone methyltransferases showed the higher number of direct interactions, while DNA methylation and demethylation the lowest number. Interestingly, histone demethylases showed strong co-expression with genes related to meristem activity and cell fate specification. While further analysis of specific interactions is ongoing, these results provide new insights into the epigenetic control of periderm formation in cork oak and lay the groundwork for future functional validation.