Chromosome-scale genome assembly clarifies the mechanism of flooding tolerance and evolutionary history of Myricaria laxiflora

Myricaria laxiflora, belonging to the Tamaricaceae family, is a valuable plant resource naturally occurring along the riverbanks of the Yangtze River Basin. In this study, we constructed a chromosome-level M. laxiflora genome which was 1.34 Gb in size, with 12 chromosomes and a contig N50 of 11.69 Mb. In total, 23,719 protein-coding genes were discovered across the M. laxiflora genome. Phylogenetic investigation indicated that Tamaricaceae and Polygonaceae diverged between 65 and 81 million years ago (Mya). M. laxiflora underwent one whole genome duplication (WGD) between 19.74 and 24.60 Mya, and experienced a long terminal repeat (LTR) insertion around 0.15 Mya. These genomic changes may be related to environmental upheavals (such as the uplift of the Qinghai-Tibet Plateau) experienced by M. laxiflora during its evolution, and also may have provided a foundation for its evolution and adaptation. To analyze the flooding adaption mechanism of M. laxiflora, we compared morphological, physiological, and transcriptomic changes under control and submerged conditions. Overall, M. laxiflora was found to adopt a "quiescence" strategy when completely submerged. Specifically, in response to submersion, photosynthesis weakens, growth stagnates, glycolysis is activated, and the antioxidant enzyme system is enhanced. The "ethylene response pathway" was ascertained as a likely regulator of this process, and a MlERF-VII gene (Mla11G026380) may be the key gene regulating this process. Our findings shed light on the underlying mechanisms behind the flooding resistance displayed by M. laxiflora, while also establishing a basis for the conservation of its genetic resources.