Water wisteria genome reveals environmental adaptation and heterophylly regulation in amphibious plants

Abstract Heterophylly is a phenomenon in which an individual plant dramatically changes its leaf shape in response to the surrounding environment. Hygrophila difformis (Acanthaceae), also known as water wisteria, has recently emerged as a model plant to study heterophylly because of its striking leaf shape variation in response to various ecological factors. Under submerged conditions, H. difformis develops complex leaves and in terrestrial conditions it develops simple leaves. Here, we sequenced and assembled the chromosome-level genome of triploid H. difformis (scaffold N50: 60.43 Mb, genome size: 871.92 Mb), which reveals 36,099 predicted protein-coding genes distributed over 15 pseudochromosomes. H. difformis diverged from its relatives during the Oligocene climate-change period and expanded the gene families related to its amphibious lifestyle. Genes involved in environmental stimuli, leaf development, and other pathways are differentially expressed in submerged and terrestrial conditions, possibly modulating morphological and physiological acclimation to changing environments. We confirmed that auxin plays a role in the heterophylly of H. difformis . Finally, we discovered candidate genes that respond to different environmental conditions and elucidated the role of LATE MERISTEM IDENTITY 1 ( LMI1 ) in heterophylly. Our study establishes H. difformis as a model for studying the interconnections between ecological adaptation and plant morphological features.