Assembly and annotation of hexaploid Sesuvium portulacastrum genome reveals insights into ion transport-mediated high-salinity adaptation

Soil salinization affects plant growth and global agricultural development, and elucidation of salt tolerance mechanisms can help to enhance crop salt resilience. We combine Oxford Nanopore Technology (ONT) sequencing and second-generation sequencing technologies to assemble a high-quality chromosome-level genome for Sesuvium portulacastrum with a total genome size of 1.69 Gb. Using nanopore sequencing and high-throughput chromosome conformation capture (Hi-C) technologies, we map this genome onto 24 chromosomes, which contain 61,420 protein-coding genes. Phylogenetic analysis shows that it is closely related to Mesembryanthemum crystallinum, diverging ∼45.2 million years ago. Genomic analyses reveal whole-genome duplication events and expanded gene families involved in ion transport and salt stress response. Transcriptomics under salt stress identifies the key tolerant gene SpHAK3, whose overexpression in Arabidopsis enhances salt tolerance. This genome provides foundational insights into hexaploid halophyte evolution and high-salinity adaptation mechanisms.