Comparative Transcriptomic and Physiological Profiling Reveals Species-Associated Differences Across Five Duckweed Species

Duckweeds (Lemnaceae) are fast-growing aquatic monocots with potential for biomass production and phytoremediation, but baseline molecular and physiological differences among species remain poorly characterized. We assembled de novo transcriptomes of five duckweed species, Lemna minor, Lemna japonica, Lemna gibba, Landoltia punctata, and Lemna aequinoctialis, grown on basal Murashige and Skoog (MS) medium (three biological replicates per species), and evaluated for completeness with Benchmarking Universal Single-Copy Orthologs (BUSCO) against Viridiplantae, Embryophyta, and Liliopsida reference sets. Orthogroup-level expression divergence was characterized by species signature scoring and Pearson correlation analysis; Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) annotations were examined using descriptive composition analyses and formal overrepresentation tests. In an independent experiment, biomass, protein content, glucose accumulation, peroxidase activity, and chlorophyll a/b concentrations were measured after 7 days under four nutrient regimes (Murashige and Skoog (MS) medium, Hoagland solution, Gamborg’s B5 medium, and nitrogen-free MS (MS–N) medium). All assemblies were highly complete (≥89% complete BUSCOs). Replicates clustered by species (median within-species r = 0.99 versus between-species r = 0.40; label-permutation p = 1 × 10−4), and species signatures selected on training replicates correctly assigned every held-out sample. GO and KEGG annotation composition differed among species, but no term reached a false discovery rate (FDR) ≤ 0.10 in species-specific enrichment tests. Medium effects were species-dependent: relative to basal MS, MS–N lowered protein and chlorophyll a and raised glucose and chlorophyll b in all species, and increased peroxidase activity in four of five species. Because the media differ in several components, these effects cannot be attributed to nitrogen alone. The five species have distinct, reproducible baseline transcriptomes and differ in their physiological responses to nutrient media, providing a hypothesis-generating resource for comparative duckweed research.