Patterns of DNA methylation changes in elite Eucalyptus clones across contrasting environments

•Epigenetic changes play an important role in the adaptation response of forest trees.•Eucalyptus is a robust system to track epigenetic changes in response to environment.•Site-specific DNA methylation changes were identified for each of five eucalypt clones.•No consistently shared epigenetic marks were found for all clones across environments.•Results showed that the observed epigenetic variation is mainly genotype dependent.