The chromosome-level genome of Water-Wisteria establishes an ecological plant model and provides insight into the molecular mechanisms underlying heterophylly in amphibious plants

SummaryThe phenomenon by which a single plant dramatically changes its leaf shape in response to the surrounding environment is called heterophylly, an ideal model for the study of plant phenotypic adaptation to environment. Hygrophila difformis (Acanthaceae), also known as Water-Wisteria, has recently merged as a model to study heterophylly due to its typical phenotypic plasticity to various ecological factors. Here, we generated a chromosome-level genome of H. difformis (scaffold N50: 57.63Mb, and genome size: 831.53 Mb) and predicted 36,099 protein-coding genes mainly on 15 pseudochromosomes. H. difformis evolved a gene expansion for its acclimation to the amphibious environment. RNA-seq analysis revealed that genes relative to environmental stimuli, leaf development and other processes are elaborated, regulating its morphological and physiological acclimations to the changing environments. Finally, we identified candidate genes under different ecological factors, and illuminated the roles of LATE MERISTEM IDENTITY 1 (LMI1) on the regulation of heterophylly in H. difformis. Our study contributes the first genome and transcriptome for Hygrophila, establishing H. difformis as a model for the relationships of ecological factors and plant morphological features. We provide new insights into the adaptability of plants in evolution, along with potential resources for trait improvement in crops.