Chromosome-Scale Genome Assemblies of Duckweeds Provide Insights Into Genomic Plasticity, Aquatic Adaptation, and Morphological Reduction

Duckweeds (Lemnaceae) present a striking example of convergent genome evolution following the return from land to water. As the smallest and fastest-growing angiosperms, they exhibit extreme morphological reduction yet retain remarkable genomic plasticity through recurrent interspecific hybridization, chromosomal rearrangements, and selective gene-family remodeling. The genomic mechanisms that distinguish this secondarily aquatic lifestyle from terrestrial ancestors, and whether these changes are convergent with other aquatic lineages such as seagrasses, have remained incompletely resolved. Here, we report chromosome-scale genome assemblies for four duckweed species, Spirodela polyrhiza, Lemna minuta, Lemna japonica, and Lemna aequinoctialis, generated with PacBio HiFi long reads and Omni-C chromatin conformation capture. These assemblies include the first genomic characterization of an unresolved hybrid lineage (L. aequinoctialis ×) that harbors a previously uncharacterized 3.5 Mb reciprocal translocation between subgenomes, as well as confirmation of the allodiploid origin of L. japonica. Comparative phylogenomics with land plants and the seagrass Zostera marina reveals a coherent, non-random program of gene loss: effector-triggered immunity components (EDS1 and PAD4) and the high-affinity nitrate transporter NRT2 are convergently absent across duckweeds and Z. marina, consistent with relaxed pathogen pressure and abundant dissolved nutrients in aquatic habitats. In contrast, secondary-metabolite biosynthesis pathways for flavonoids, anthocyanins, flavones, and flavonols are retained or expanded despite overall genome compaction. These findings illustrate how the return to aquatic environments following terrestrialization shaped duckweed genome evolution through convergent gene loss and selective pathway retention, and provide high-quality genomic resources to support future research in plant evolutionary biology and biotechnology.