Soil salinity is a growing concern for global crop production and the sustainable development of humanity. Therefore, it is crucial to comprehend salt tolerance mechanisms and identify salt-tolerance genes to enhance crop tolerance to salt stress. Suaeda glauca, a halophyte species well adapted to the seawater environment, possesses a unique ability to absorb and retain high salt concentrations within its cells, particularly in its leaves, suggesting the presence of a distinct mechanism for salt tolerance. In this study, we performed de novo sequencing of the S. glauca genome. The genome has a size of 1.02 Gb (consisting of two sets of haplotypes) and contains 54 761 annotated genes, including alleles and repeats. Comparative genomic analysis revealed a strong synteny between the genomes of S. glauca and Beta vulgaris. Of the S. glauca genome, 70.56% comprises repeat sequences, with retroelements being the most abundant. Leveraging the allele-aware assembly of the S. glauca genome, we investigated genome-wide allele-specific expression in the analyzed samples. The results indicated that the diversity in promoter sequences might contribute to consistent allele-specific expression. Moreover, a systematic analysis of the ABCE gene families shed light on the formation of S. glauca’s flower morphology, suggesting that dysfunction of A-class genes is responsible for the absence of petals in S. glauca. Gene family expansion analysis demonstrated significant enrichment of Gene Ontology (GO) terms associated with DNA repair, chromosome stability, DNA demethylation, cation binding, and red/far-red light signaling pathways in the co-expanded gene families of S. glauca and S. aralocaspica, in comparison with glycophytic species within the chenopodium family. Time-course transcriptome analysis under salt treatments revealed detailed responses of S. glauca to salt tolerance, and the enrichment of the transition-upregulated genes in the leaves associated with DNA repair and chromosome stability, lipid biosynthetic process, and isoprenoid metabolic process. Additionally, genome-wide analysis of transcription factors indicated a significant expansion of FAR1 gene family. However, further investigation is needed to determine the exact role of the FAR1 gene family in salt tolerance in S. glauca.

Nitrogen (N) is crucial for plant growth and stress resistance and is primarily absorbed and transported by nitrate transporters (NRT). Suaeda glauca, known for its strong salt-alkali stress resistance, and SgNRT genes have rarely been reported. This study aims to identify and analyze the SgNRT gene family to understand its composition, evolutionary patterns, and roles in salt stress responses. We identified 212 SgNRTs, which were categorized into three branches, with SgNRT1/SgNPF and SgNRT2 as the major families. Structural analysis, conserved domains, chromosomal localization, and collinearity were also examined. Spatiotemporal expression characteristics of SgNRT genes were analyzed, revealing specific expression across 13 organs or tissues and dynamic responses to salt treatment over 48 h. Notably, SgNRT1.185, SgNRT2.25, and SgNRT2.2 exhibited rapid salt induction in leaves (activated within 0.5 h, peaking at 2 h), with SgNRT1.185 showing relatively high upregulation. SgNRT1.185 and SgNRT2.35 were induced by high salt concentrations (200 mM) in both roots and leaves. SgNRT2.35 exhibited higher basal and stress-induced levels than the other genes. Bioinformatics analysis suggests spatially specific expression of SgNRT genes, potentially involved in nitrogen absorption and transport across various developmental stages and organs/tissues of Suaeda glauca. These findings offer a theoretical basis for understanding the adaptive strategies of Suaeda glauca under saline-alkali stress and provide insights into the functional evolution of plant NRT genes, aiding in the development of stress-resistant crops.