Title : Evolutionary epigenomics of mangroves reveals the homeostatic role of gene body methylation in stress adaptation
DNA methylation plays an important role in plant stress responses whereas little is known about its role in long-term stress adaptation. In this study, we used mangroves well-adapted to tropical intertidal environments as a model system to understand the role of gene body methylation, i.e., CG methylation in coding regions, in plant stress adaptation. Using whole-genome bisulfite sequencing, we compared patterns of gene body methylation between pairs of mangrove and non-mangrove species using rice as outgroup. We found massive gains of gene body methylation specific to mangrove lineages. The estimated gain-to-loss ratio of gene body methylation in mangroves is magnitudes higher than that in non-mangroves. We estimated that more than a thousand genes exhibited convergent body methylation in mangrove genomes (convBMM) but only tens of genes in the non-mangroves (convBMN). In comparison with non-convergent gbM genes, covBMM but not convBMN genes showed reduced gene expression variation in response to salt and UV-B stresses. We found little overlap between convBMM genes and loci with signatures of convergent DNA sequence evolution. Our results suggest that positive selection acts on natural gbM variation to increase gene expression stability. This may allow rapid accumulation of genetic variation and thus accelerate long-term adaptation to environmental stresses.
Take Away Notes:
• This study indicates that epigenetics independent of genetics plays a significant role in adaptive evolution.
• Our results suggest that gene expression homeostasis is crucial for plant long-term adaptation to environmental stresses.
• Genes with mangrove-specific convergent gene body methylation would provide a valuable resource for unraveling the molecular mechanisms underlying plant adaptation in general.