Ecological plant epigenetics: Evidence from model and non-model species, and the way forward

Abstract

Growing evidence makes a strong case that epigenetic mechanisms contribute to complex traits, with implications across many fields of biology from dissecting developmental processes to understanding aspects of human health and disease. In ecology, recent studies have merged ecological experimental design with epigenetic analyses to elucidate the contribution of epigenetics to plant phenotypes, stress response, adaptation to habitat, or species range distributions. While there has been some progress in revealing the role of epigenetics in ecological processes, many studies with non-model species have so far been limited to describing broad patterns based on anonymous markers of DNA methylation. In contrast, studies with model species have benefited from powerful genomic resources, which allow for a more mechanistic understanding but have limited ecological realism. To understand the true significance of epigenetics for plant ecology and evolution, we must combine both approaches transferring knowledge and methods from model-species research to genomes of evolutionarily divergent species, and examining responses to complex natural environments at a more mechanistic level. This requires transforming genomics tools specifically for studying non-model species, which is challenging given the large and often polyploid genomes of plants. Collaboration between molecular epigeneticists, ecologists and bioinformaticians promises to enhance our understanding of the mutual links between genome function and ecological processes.All rights reserved. No reuse allowed without permission.(which was not peer-reviewed) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity.

Climate Change Impacts on Seagrass Meadows and Macroalgal Forests: An Integrative Perspective on Acclimation and Adaptation Potential

“…Epigenetics research is growing particularly strong in terrestrial plants (Hirsch et al, 2013;Slotkin, 2016;Richards et al, 2017). A case in point within the context of climate change, is thermal tolerance that may be partly ascribed to CG methylationvariants, which is supported by temperature-associated variation in gene-body methylation in natural populations of A. thaliana (Dubin et al, 2015;Keller et al, 2016) and the valley oak Quercus lobata (Gugger et al, 2016).…”

“…Epigenetic variations are molecular modifications that alter gene expression, but not the underlying DNA sequence, and occur in the form of histone modifications, non-coding RNAs, and DNA methylations (Bossdorf et al, 2008;Berger et al, 2009). Recent studies in the young research field of Ecological Epigenetics provide increasing evidence for the potential of epigenetic variation to increase plasticity, facilitate speciation and accelerate adaptation to new environments and stressful conditions (Schrey et al, 2013;Bonasio, 2015;Verhoeven et al, 2016;Kilvitis et al, 2017;Richards et al, 2017).…”

“…Seagrasses likely show methylation in the same three sequence contexts as terrestrial plants, including CHG, CHH, and CG (Xie and Yu, 2015;Kilvitis et al, 2017;Richards et al, 2017). So-called CpG islands represent clusters of CG sites in gene promoter regions, and are commonly associated with gene expression regulation (Bossdorf et al, 2008;Illingworth and Bird, 2009;Zhang and Jeltsch, 2010).…”

“…DNA-methylation variants (epialleles), epigenetic modifications that involve the addition of a methyl-group to cytosines (5-mC) in DNA sequence motifs, are currently the most popular epigenetic modification screened in evolutionary and ecological contexts (Schrey et al, 2013;Verhoeven et al, 2016;Richards et al, 2017). The possibility of methylation changes to respond directly to environmental change, and to trigger at least partly heritable changes in gene expression, resembles Lamarck's theory of the inheritance of acquired characteristics (Schmitz et al, 2013;Herman and Sultan, 2016) and ultimately challenges the classical theory of evolutionary adaptation.…”

Innovatieve methodes voor natuurbeheer: moleculair genetische technieken voor soortenbescherming en -beheer

“…Via het aan-of uitschakelen van genen heeft epigenetische variatie een invloed op het fenotype van een individu. Steeds meer studies tonen aan dat epigenetische variatie kan doorgegeven worden aan opeenvolgende generaties en op die manier ook een rol speelt in het aanpassingsvermogen en evolutiepotentieel van populaties (voor een overzicht zie Richards et al, 2017). Dit is vermoedelijk vooral het geval bij soorten die zich ongeslachtelijk voortplanten en bij lang levende organismen (Gonzalez et al, 2017;Latzel et al, 2016;Verhoeven & Preite, 2014).…”