Suaeda salsa L. is a typical halophyte with high value as a vegetable. Here, we report a 447.98 Mb, chromosomal-level genome of S. salsa, assembled into nine pseudomolecules (contig N50 = 1.36 Mb) and annotated with 27,927 annotated protein-coding genes. Most of the assembled S. salsa genome, 58.03%, consists of transposable elements. Some gene families including HKT1, NHX, SOS and CASP related to salt resistance were significantly amplified. We also observed expansion of genes encoding protein that bind the trace elements Zn, Fe, Cu and Mn, and genes related to flavonoid and α-linolenic acid metabolism. Many expanded genes were significantly up-regulated under salinity, which might have contributed to the acquisition of salt tolerance in S. salsa. Transcriptomic data showed that high salinity markedly up-regulated salt-resistance related genes, compared to low salinity. Abundant metabolic pathways of secondary metabolites including flavonoid, unsaturated fatty acids and selenocompound were enriched, which indicates that the species is a nutrient-rich vegetable. Particularly worth mentioning is that there was no significant difference in the numbers of cis-elements in the promoters of salt-related and randomly selected genes in S. salsa when compared with Arabidopsis thaliana, which may affirm that plant salt tolerance is a quantitative rather than a qualitative trait in terms of promoter evolution. Our findings provide deep insight into the adaptation of halophytes to salinity from a genetic evolution perspective.
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