Unusual predominance of maintenance DNA methylation in Spirodela polyrhiza

Abstract

Abstract5-methylcytosine (5mC) is a modified base often described as necessary for the proper regulation of genes and transposons and for the maintenance of genome integrity in plants. However, the extent of this dogma is limited by the current phylogenetic sampling of land plant species diversity. Here, we report that a monocot plant, Spirodela polyrhiza, has lost CG gene body methylation, genome-wide CHH methylation, and the presence or expression of several genes in the highly conserved RNA-directed DNA methylation (RdDM) pathway. It has also lost the CHH methyltransferase CHROMOMETHYLASE 2. Consequently, the transcriptome is depleted of 24-nucleotide, heterochromatic, small interfering RNAs that act as guides for the deposition of 5mC to RdDM-targeted loci in all other currently sampled angiosperm genomes. Although the genome displays low levels of genome-wide 5mC primarily at LTR retrotransposons, CG maintenance methylation is still functional. In contrast, CHG methylation is weakly maintained even though H3K9me2 is present at loci dispersed throughout the euchromatin and highly enriched at regions likely demarcating pericentromeric regions. Collectively, these results illustrate that S. polyrhiza is maintaining CG and CHG methylation mostly at repeats in the absence of small RNAs. S. polyrhiza reproduces rapidly through clonal propagation in aquatic environments, which we hypothesize may enable low levels of maintenance methylation to persist in large populations.Significance StatementDNA methylation is a widespread chromatin modification that is regularly found in all plant species. By examining one aquatic duckweed species, Spirodela polyrhiza, we find that it has lost highly conserved genes involved in methylation of DNA at sites often associated with repetitive DNA, and within genes, however DNA methylation and heterochromatin is maintained during cell division at other sites. Consequently, small RNAs that normally guide methylation to silence repetitive DNA like retrotransposons are diminished. Despite the loss of a highly conserved methylation pathway, and the reduction of small RNAs that normally target repetitive DNA, transposons have not proliferated in the genome, perhaps due in part to the rapid, clonal growth lifestyle of duckweeds.

Atypical epigenetic and small RNA control of transposons in clonally reproducingSpirodela polyrhiza

“…and DECREASE IN DNA METHYLATION 1 (DDM1) orthologues were found present and expressed in Spirodela, albeit at a lower degree than in Arabidopsis. On the contrary, CMT2, required to maintain mCHH together with SUVH4 [23], is missing as previously reported [73] (Fig. 2e, Supplemental Fig.…”

“…Furthermore, several sRNA silencing components including some involved in RdDM have been shown to be missing, low or not expressed. In addition, CMT2, which maintains CHH methylation, is lost [37][38][39].…”

DNA methylation in clonal duckweed (Lemna minor L.) lineages reflects current and historical environmental exposures

“…The patterns observed in duckweed are different: CHG and CG are the primary cytosine contexts whose methylation level responds to stress exposure, not CHH. In the closely related Spirodela polyrhiza , partial and complete loss of genes involved in the DNA methylation pathway have been demonstrated (Harkess et al, 2020 ). This loss has led to a drastic decrease in genome‐wide methylation in all three cytosine contexts, and especially in CHH context (~10% CG, ~3.3% CHG and ~0.1% CHH) as well as a loss in CG gene‐body methylation compared to what is normally observed in land plants.…”

DNA methylation in clonal Duckweed lineages (Lemna minorL.) reflects current and historical environmental exposures

“…The patterns observed in Duckweed are different: CHG and CG are the primary cytosine contexts whose methylation level responds to stress exposure, not CHH. In the closely related Spirodela polyrhiza , partial and complete loss of genes involved in the DNA methylation pathway have been demonstrated (Harkess et al, 2020). This loss has led to a drastic decrease in genome-wide methylation in all 3 cytosine contexts (~10% CG, ~3.3% CHG and ~0.1% CHH) as well as a loss in CG gene-body methylation compared to what is normally observed in land plants.…”