Environmental and genealogical effects on DNA methylation in a widespread apomictic dandelion lineage

DNA methylation in plant genomes occurs in different sequences and genomic contexts that have very different properties. DNA methylation that occurs in CG (mCG) sequence context shows transgenerational stability and high epimutation rate, and can thus provide genealogical information at short time scales. However, due to meta‐stability and because mCG variants may arise due to other factors than epimutation, such as environmental stress exposure, it is not clear how well mCG captures genealogical information at micro‐evolutionary time scales. Here, we analysed DNA methylation variation between accessions from a geographically widespread, apomictic common dandelion (Taraxacum officinale) lineage when grown experimentally under different light conditions. Using a reduced‐representation bisulphite sequencing approach, we show that the light treatment induced differentially methylated cytosines (DMCs) in all sequence contexts, with a bias towards transposable elements. Accession differences were associated mainly with DMCs in CG context. Hierarchical clustering of samples based on total mCG profiles revealed a perfect clustering of samples by accession identity, irrespective of light conditions. Using microsatellite information as a benchmark of genetic divergence within the clonal lineage, we show that genetic divergence between accessions correlates strongly with overall mCG profiles. However, our results suggest that environmental effects that do occur in CG context may produce a heritable signal that partly dilutes the genealogical signal. Our study shows that methylation information in plants can be used to reconstruct micro‐evolutionary genealogy, providing a useful tool in systems that lack genetic variation such as clonal and vegetatively propagated plants. DNA methylation in plant genomes occurs in different sequences and genomic contexts that have different properties. Using accessions from one asexually reproducing dandelion lineage, we evaluated how long‐term methylation differences build up, and how these compare to short‐term environmental effects on methylation. Genealogy of the accessions was captured well by DNA methylation in CpG dinucleotides, which shows high transgenerational stability and epimutation rates in plants. Methylation effects of experimental light treatments occurred both in CpG and in non‐CpG contexts. The latter are transient but the former can produce a heritable signal that may dilute the genealogical signal.