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Unusual predominance of maintenance DNA methylation in Spirodela polyrhiza

ABSTRACT: Unusual predominance of maintenance DNA methylation in Spirodela polyrhiza

PROVIDER: PRJNA675910 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR13021604.fastq.gz	Fastqsanger.gz
	SRR13021605.fastq.gz	Fastqsanger.gz
	SRR13021606.fastq.gz	Fastqsanger.gz
	SRR13021607.fastq.gz	Fastqsanger.gz
	SRR13021608.fastq.gz	Fastqsanger.gz

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Unusual predominance of maintenance DNA methylation in Spirodela polyrhiza

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.

2022-08-24 | GSE161234 | GEO

Spirodela polyrhiza root and frond phosphate starvation RNA-Seq

Project description:Spirodela polyrhiza (9509) was grown under replete conditions for 10d, subject to media without phosphate or control for 24h, and then sequenced.

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The unusual predominance of maintenance DNA methylation in Spirodela polyrhiza.

Project description:Duckweeds are among the fastest reproducing plants, able to clonally divide at exponential rates. However, the genetic and epigenetic impact of clonality on plant genomes is poorly understood. 5-methylcytosine (5mC) is a modified base often described as necessary for the proper regulation of certain 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 analyzed DNA methylomes, small RNAs, mRNA-seq, and H3K9me2 histone modification for Spirodela polyrhiza. S. polyrhiza has lost highly conserved genes involved in de novo methylation of DNA at sites often associated with repetitive DNA, and within genes, however, symmetrical DNA methylation and heterochromatin are maintained during cell division at certain transposons and repeats. 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.

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