A Chromosome-Level Genome Sequence Reveals Regulation of Salt Stress Response in Mesembryanthemum crystallinum

Salt stress disturbs plant growth and photosynthesis due to its toxicity. The ice plant Mesembryanthemum crystallinum is a highly salt-tolerant facultative crassulacean acid metabolism (CAM) plant. However, the genetic basis of the salt tolerance mechanisms in ice plants remains unclear. In this study, we constructed a chromosome-level whole-genome sequence of the ice plant and performed transcriptome analysis of the effects of salt treatment on the leaves. After 24-hour 500 mM NaCl treatment to the roots, 1100 and 1394 genes, including CAM pathway, glycolysis, and inositol metabolism, were up- and down-regulated in the leaves, respectively. Salt treatment also influenced the abscisic acid (ABA) signaling components, including genes from the PYRABACTIN RESISTANCE1 (PYR1) family and the PROTEIN PHOSPHATASE 2CA (PP2CA) family. We detected the induction of the genes encoding various ion transporters after salt treatment. The expression of most v-ATPase subunits is induced, leading to vacuolar acidification, which facilitates sodium ion sequestration in the vacuoles. Additionally, some genes encoding metal ion transporters, including the genes from the ZIP family and NRAMP family, were induced by salt treatment, accompanied by the accumulation of iron, zinc, and copper ions in the leaves. Cis-motif enrichment analysis revealed that ABRE-like motifs and MYB-binding-like motifs were enriched in the upstream sequences of genes that were either up-regulated or down-regulated by salt. In conclusion, this study highlights how salt treatment induces drastic and rapid transcriptomic changes and unveils the ice plant's genomic foundation. Our resources provide further insights into the regulation of salt tolerance in the ice plants.