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Duckweeds (Lemnaceae) are the smallest and fastest-growing flowering plants. Their clonal lifestyle, miniaturized body plan, and growing value for the circular bioeconomy, from wastewater remediation and carbon capture to bio-based protein and starch production for food, feed and fuel, make them attractive both as models for plant biology and as platforms for biotechnology.
We first used the giant duckweed Spirodela polyrhiza, compact genome similar to that of Arabidopsis, to ask how transposable elements (TEs) are kept in check in a plant with strikingly low DNA methylation, a near-absence of 24-nt siRNAs, and the loss of several canonical RNA-directed DNA methylation (RdDM) and silencing genes. We find that abundant, degenerated TEs have reduced or absent DNA methylation and H3K9me2 yet remain heterochromatic through H3K9me1, whereas
the few intact TEs retain DNA methylation and 24-nt siRNA production, evidencing that heterochromatin can be maintained independently of DNA methylation in flowering plants and the selective recognition of potentially mobile TEs by RdDM. Comparison with the TE-rich (~75%) duckweed Wolffia brasiliensis shows that recent TE expansion had dramatic consequences for the genome architecture and that, despite a shared silencing toolbox, transposon expansion reshapes small RNA deployment and methylation landscapes, underscoring the central role of TEs in structuring epigenomes.
Building on this biology, we overcame a long-standing bottleneck by establishing a reproducible Agrobacterium-mediated transformation and CRISPR/Cas9 genome-editing platform for Spirodela and have expanded this toolset to other duckweeds. Unexpectedly, Spirodela does not mount an effective silencing response against
transgenes: both transient and stable transgenes remain active for weeks or hundreds of clonal generations without triggering sense post-transcriptional gene silencing (S-PTGS) or transgene-derived siRNAs. Our ongoing work links this to an apparent loss of small RNA amplification and secondary siRNA biogenesis. I will discuss how this absence of transgene silencing simultaneously illuminates the evolution of small RNA pathways and provides a uniquely “silencing-free” chassis for duckweed biotechnology.
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