Project description:Spirodela polyrhiza (9509) was grown under replete conditions for 10d, subject to media without phosphate or control for 24h, and then sequenced.
Project description:In flowering plants, silencing of transposable elements (TEs) is achieved by the installation of DNA methylation and histone modifications. 24-nt long small-interfering RNAs (siRNAs) guide the deposition of DNA methylation through RNA-directed DNA methylation (RdDM), which can be maintained independently of siRNAs in coordination with H3K9me2. In most angiosperms, RdDM is ubiquitously expressed in vegetative and sexual reproductive tissues. Spirodela polyrhiza (Lemnaceae), represents an exception with low levels of DNA methylation, very low expression of RdDM and near absence of 24-nt siRNAs during its clonal vegetative propagation. Moreover, some components of RdDM, DNA methylation maintenance and RNA silencing are absent from the genome. By investigating the distribution of epigenetic marks on TEs, we show that Spirodela epigenome is shaped by the loss of DNA methylation and H3K9me2 as TEs decay. Nonetheless, such abundant TE remnants remain silenced and marked by H3K9me1. In contrast, scarce, relatively intact TEs display high levels of DNA methylation, H3K9me2 and siRNAs whose patterns resemble those of TEs subjected to RdDM in other angiosperms. Furthermore, despite the absence of DCL2 in duckweeds, Spirodela can produce 22-nt siRNAs, not only from TEs, but from diverse sources of double-stranded (ds)RNA. Our data suggests that RdDM might still be functional during vegetative clonal growth, albeit tissue or developmentally regulated, and highlights the use of alternative models to further understand and explore the diversity of silencing pathways in plants.
Project description:5-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. 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.
