The ability to respond to varying environments is crucial for sessile organisms such as plants. The amphibious plant Rorippa aquatica exhibits a striking type of phenotypic plasticity known as heterophylly, a phenomenon in which leaf form is altered in response to environmental factors. However, the underlying molecular mechanisms of heterophylly are yet to be fully understood. To uncover the genetic basis and analyze the evolutionary processes driving heterophylly in R. aquatica, we assembled the chromosome-level genome of the species. Comparative chromosome painting and chromosomal genomics revealed that allopolyploidization and subsequent post-polyploid descending dysploidy occurred during the speciation of R. aquatica. Based on the obtained genomic data, the transcriptome analyses revealed that ethylene signaling plays a central role in regulating heterophylly under submerged conditions, with blue light signaling acting as an attenuator of ethylene signal. The assembled R. aquatica reference genome provides insights into the molecular mechanisms and evolution of heterophylly.

CEITEC Central European Institute of Technology Masaryk University CZ 625 00 Brno Czech Republic

Center for Plant Sciences Kyoto Sangyo University Kamigamo Motoyama Kita ku Kyoto Japan

Department of Applied Biological Science Faculty of Science and Technology Tokyo University of Science 2641 Yamazaki Noda Chiba Japan

Department of Horticulture Faculty of Agriculture University of Maragheh Maragheh Iran

Department of Integrated Biosciences Graduate School of Frontier Science The University of Tokyo Chiba Japan

Department of Plant Biology University of California Davis One Shields Avenue Davis CA USA

Faculty of Life Sciences Kyoto Sangyo University Kamigamo Motoyama Kita ku Kyoto Japan

Faculty of Science Kanagawa University 3 27 1 Rokkakubashi Kanagawa ku Yokohama Kanagawa Japan

Graduate School of Science Department of Biological Sciences The University of Tokyo Science Build 2 7 3 1 Hongo Bunkyo ku Tokyo Japan

The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences Institute of Hydrobiology Chinese Academy of Sciences Wuhan Hubei China

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