The unusual predominance of maintenance DNA methylation in Spirodela polyrhiza

Abstract 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 o...

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Bibliographic Details
Published in:G3 : genes - genomes - genetics 2024-04, Vol.14 (4)
Main Authors: Harkess, Alex, Bewick, Adam J, Lu, Zefu, Fourounjian, Paul, Michael, Todd P, Schmitz, Robert J, Meyers, Blake C
Format: Article
Language:English
Subjects:
DNA
DNA Methylation
Genome, Plant
Heterochromatin
Investigation
Phylogeny
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Summary:Abstract 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. Duckweeds are among the fastest reproducing plants on the planet. One species, Spirodela polyrhiza, has lost key genes involved in de novo methylation of DNA at sites often associated with repetitive DNA, and within genes. However symmetrical DNA methylation and heterochromatin is maintained.
ISSN:2160-1836
2160-1836
DOI:10.1093/g3journal/jkae004