Unraveling salt-responsive genes in Suaeda salsa through genomic and transcriptomic profiling across salinity gradients.

Salinity severely limits global crop productivity, prompting a need to uncover plant salinity adaptation strategies. Suaeda salsa (L.) Pall., a halophyte thriving in saline habitats, offers a valuable model to dissect plant growth mechanisms under saline conditions. Although a chromosome-level reference genome of S. salsa was recently published, the corresponding gene annotation remained unavailable. Using the Helixer tool, we generated and released the first publicly available genome annotation for S. salsa, exhibiting high completeness with 92.80% (1,498) complete BUSCOs, thus providing an essential genomic resource. Using the S. salsa reference genome and annotation, we conducted RNA-seq-based transcriptomic profiling of plants subjected to 0, 200, and 400 mM NaCl for 30 days, respectively. We identified 462 significantly differentially expressed annotated genes across all treatments, with 11 key candidates consistently regulated. These genes are involved in key salinity response-related processes, including ion transport, osmotic adjustment, antioxidant defense, hormone signaling, transcriptional regulation, and genome plasticity. Enrichment analyses further supported their roles in ion homeostasis, redox regulation, and metabolic adjustment. This study provides new insights into the long-term salt tolerance mechanisms of S. salsa during normal development. The findings lay a foundation for future functional studies, comparative evolutionary analyses, and genetic improvement of salt-tolerant crops.