Unraveling the mysteries of duckweed: epigenetic insights from Spirodela polyrhiza

A formidable invader of freshwater bodies, duckweed’s ability to thrive in diverse environments is a remarkable display of resilience, especially considering its small genome size and lack of sexual reproduction. Duckweed—the common name for members of the Lemnaceae family of monocots—defies conventional reproductive norms through clonal propagation. New individuals sprout from a single parent, bypassing the need for sexual reproduction and allowing for the fast reproduction that underlies their invasiveness.

Research recently published in G3: Genes|Genomes|Genetics delves into DNA methylation in the duckweed Spirodela polyrhiza, exploring its implications for clonal propagation and shedding light on the intricacies of plant biology.

Duckweed’s resilience hints at the intricate role epigenetic variation plays in shaping the plant kingdom’s evolution. Epigenetic modifications, particularly DNA marks like 5-methylcytosine (5mC), play pivotal roles in regulating gene expression and genome stability in plants. But duckweed deviates from the norm for plants, exhibiting notably low levels of 5mC.

Prompted by this intriguing anomaly, Harkess, Bewick, et al., set out to better understand the genetic and epigenetic impact that clonal propagation has on duckweed.

In plants, DNA methylation occurs in three sequence contexts: CG, CHG, and CHH (where H = A, C, T). It is initiated by the highly conserved RNA-directed DNA methylation (RdDM) pathway, which generates 24-nucleotide heterochromatic siRNAs via processing of double-stranded RNAs by DICER-LIKE 3 (DCL3). Subsequently, maintenance methyltransferases like MET1, CMT2, and CMT3 ensure the preservation of methylation during DNA replication.

However, key players of the RdDM pathway are notably absent in duckweed, as is the CMT2 maintenance methlytransferase. These absences have profound implications, particularly at CHH sites, where methylation is significantly reduced.

Interestingly, this phenomenon extends beyond duckweed, with related species Landoltia punctata, Lemna minor, and the aquatic seagrass Zostera marina exhibiting a similar absence of methylation machinery. The loss of these methylation players may represent a shared evolutionary adaptation among aquatic plants, potentially conferring advantages in varied climates and stresses.

The authors also report the absence of transposon proliferation in the S. polyrhiza genome, despite the loss of highly conserved genes involved in CHH methylation, prompting them to speculate on the role of CHH methylation in silencing transposons in asexual species. They suggest that clonally propagated species may rely more heavily on maintenance methylation mechanisms, rendering CHH methylation unnecessary for transposon suppression. Based on the research, it appears that losing CHH-type methylation and heterochromatic siRNAs may benefit duckweed by facilitating rapid asexual reproduction. The authors suggest that duckweed’s reproductive efficiency through quick clonal propagation might be enhanced by foregoing the RdDM and CMT2 pathway. Duckweed serves as a captivating case study in plant biology, offering invaluable insights into the intricate interplay between epigenetics, evolution, and environmental adaptation. As researchers continue to unravel its mysteries, the implications for agriculture, ecology, and beyond are boundless.