Genomic insights into flooding tolerance of <i>Distylium chinense</i> in the water‐level fluctuation zone of the Three Gorges Reservoir

The intensification of climate change has led to frequent extreme flooding events, which threaten plant growth and food security. Studying the molecular mechanisms underlying plant flooding resistance is crucial for germplasm improvement. Distylium chinense, a perennial shrub found in the water-level fluctuation zone of the Three Gorges Reservoir, has both strong flooding tolerance and high ornamental value, making it an ideal material for studying plant flooding resistance mechanisms. By integrating multiple sequencing technologies, we assembled a high-quality 917 Mb near telomere-to-telomere genome of D. chinense with a contig N50 size of 73 Mb, representing the first high-quality genome of the Hamamelidaceae family. Whole-genome duplication analysis revealed that D. chinense experienced gamma events that are common to those of core eudicots. In addition, this study revealed three different flooding stress response stages in D. chinense, namely, the acute stress period, the outbreak period, and the long-term adaptation period. Among these, the outbreak period could be an important turning point, during which D. chinense switches from survival mode to adaptation mode. This study also revealed that the expression of the group VII ethylene-responsive factor (ERF-VII) gene g3958 was significantly upregulated under flooding stress and that this gene can be directly activated by the AtWRKY33-homologous gene g19705. On the basis of a comprehensive analysis, a potential dual pathway regulatory model between MKK9 and ERF-VII was further proposed. This study provides important genetic resources for improving flood-resistant germplasms and further contributes to the protection and restoration of the ecosystem in the water-level fluctuation zone of the Three Gorges Reservoir.