Aquatic plants are specialized evolutionary groups adapted to life in water. They play critical roles as food and medicinal supplies (e.g., lotus root and foxnut) and industrial raw materials (e.g., reeds), as well as in ecological restoration. While most aquatic lineages have independently evolved from terrestrial ancestors, the genomic dynamics underlying this adaptation remain largely unexplored.
To address this knowledge gap, a research team from the Wuhan Botanical Garden of the Chinese Academy of Sciences, in collaboration with China Pharmaceutical University, integrated whole-genome assemblies of 122 vascular plant species with morphological analyses (including analyses of stomata, vascular bundles, and aerenchyma), waterlogging experiments, and transcriptome sequencing.
The study, which was recently published in Current Biology, reveals convergent genomic dynamics that drive plants' adaptation to aquatic environments.
The researchers compared the evolutionary rates of genes across species representing different life forms: terrestrial plants, emergent/floating-leaved plants, freshwater submerged plants, and seagrasses. They found that aquatic plants-especially submerged species and seagrasses-show significantly higher evolutionary rates in their nuclear, mitochondrial, and chloroplast genes. These rates are notably higher than those of their terrestrial relatives. This suggests that aquatic environments do not "slow dow" evolution; instead, they may accelerate genomic changes-either through ecological constraints (e.g., low light, hypoxia, and salinity fluctuations) that boost mutation rates or via small population effects that promote genetic drift.
Furthermore, the study uncovered extensive convergent expansions of gene families across diverse aquatic plant lineages，arguing againstthe widely held view that aquatic plants adapt to water primarily through gene loss and genome streamlining. These expanded genes are closely linked to key adaptive traits, including iron ion homeostasis, aerenchyma formation, enhanced photosynthesis, and osmoregulation. For example, the transcription factor bHLH115-responsible for iron deficiency responses-has expanded remarkably in submerged species, likely enhancing their ability to adapt to iron-deficient aquatic environments.
Microscopic observations and controlled experiments also revealed notable differences in stomatal development and aerenchyma formation among various aquatic plants. For instance, submerged plants typically lack stomata or have reduced stomata on their underwater leaves; however, some species can rapidly develop stomata when exposed to air, demonstrating strong phenotypic plasticity. Further analysis showed a significant positive correlation between the copy numbers of 13 key stomatal-development genes and the total stomatal area per unit leaf area.
By comparing gene expression variations between submerged and aerial conditions in 12 representative species (encompassing terrestrial, emergent/floating-leaved, and submerged types), the team found that emergent/floating-leaved species and terrestrial plants activate a specific set of genes (e.g., those related to ethylene synthesis, hypoxia tolerance, and aerenchyma formation) to "resist" or "escape" flooding stress. In contrast, submerged plants displayed a distinctly different expression pattern: Genes associated with stomatal development and cell-wall synthesis were significantly upregulated when leaves were exposed to air, but these pathways were suppressed when the plants grew underwater. This indicates that after long-term evolution, submerged plants may have shifted from a "stress response" strategy to a state of "full adaptation."
Global climate change is triggering more frequent and severe flooding events, which pose a serious threat to food security, the researchers noted. By unraveling the genomic mechanisms that enable aquatic plants to thrive in water, the researchers aim to develop strategies to enhance crop resilience to flooding, ultimately ensuring a more stable food supply amid ongoing climate change.
