Opportunities and limitations of reduced representation bisulfite sequencing in plant ecological epigenomics

Abstract

Contents Summary 738 I. Introduction 738 II. RRBS loci as genome-wide epigenetic markers 739 III. Exploiting functional annotation of RRBS loci 739 IV. Limitations of RRBS methods for nonmodel species 740 V. Maximising the impact of RRBS in plants 741 VI. Conclusions 741 Acknowledgements 741 SUMMARY: Investigating the features and implications of epigenetic mechanisms across the breadth of organisms and ecosystems is important for understanding the ecological relevance of epigenetics. Several cost-effective reduced representation bisulfite sequencing approaches (RRBS) have been recently developed and applied to different organisms that lack a well annotated reference genome. These new approaches improve the assessment of epigenetic diversity in ecological settings and may provide functional insights. We assess here the opportunities and limitations of RRBS in nonmodel plant species. Well thought out experimental designs that include complementary gene expression studies, and the improvement of genomics resources for the target group, promise to maximize the effect of future RRBS studies.

Keywords: DNA methylation; adaptation; bisulfite sequencing; bsRADseq; ecological genomics; epiGBS; reduced representation bisulfite sequencing (RRBS); response to environment.

Figure 1

Typically, studies in ecological epigenetics will be interested in methylation differences that are associated with two different environmental conditions as shown in this cartoon. Reduced representation bisulfite sequencing (RRBS) data can provide functional insight in non-model species (e.g. the left most RRBS locus), but detecting the genomic context of RRBS fragments is difficult in the absence of a reference genome. In addition, the number of cytosines contained per RBBS locus may be insufficient to call differentially methylated regions (DMRs), hence RRBS analyses will be limited to calling differentially methylated positions (DMPs). TE - transposable element.