Comparative Transcriptomic and Physiological Profiling Reveals Species-Associated Differences Across Five Duckweed Species
- 1Department of Biological Sciences, Clemson University, 132 Long Hall, Clemson, SC 29634, USA
- 2Department of Genetics & Biochemistry, Clemson University, 105 Collings St., Biosystems Research Complex, Clemson, SC 29634, USA
Abstract
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.
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BibTeX
@article{thingujam2026comparative,
title = {{Comparative Transcriptomic and Physiological Profiling Reveals Species-Associated Differences Across Five Duckweed Species}},
author = {Doni Thingujam and Zhengzhi Tan and Yiqing Wang and Karolina M. Pajerowska-Mukhtar and M. Shahid Mukhtar},
journal = {International Journal of Molecular Sciences},
year = {2026},
month = oct,
doi = {10.3390/ijms27219681},
url = {https://www.mdpi.com/1422-0067/27/21/9681},
note = {CC BY 4.0},
}
RIS
TY - JOUR
TI - Comparative Transcriptomic and Physiological Profiling Reveals Species-Associated Differences Across Five Duckweed Species
AU - Doni Thingujam
AU - Zhengzhi Tan
AU - Yiqing Wang
AU - Karolina M. Pajerowska-Mukhtar
AU - M. Shahid Mukhtar
PY - 2026
DA - 2026/10/29
JO - International Journal of Molecular Sciences
DO - 10.3390/ijms27219681
UR - https://www.mdpi.com/1422-0067/27/21/9681
AB - 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.
SN - 1422-0067
ER -