Molecular evolutionary analysis and expression patterns of nitrogen assimilation-related gene families in <i>Lycium ruthenicum</i> under salt stress

Nitrogen assimilation plays a critical role in the response of plants to salt stress. In this study, bioinformatics and computational biology methods were employed to identify members of the <italic>Lycium GS</italic>, <italic>GOGAT</italic>, and <italic>GDH</italic> gene families, and analyzed their expression patterns and transcriptional regulatory networks under salt stress in black wolfberry (<italic>Lycium ruthenicum</italic>). In addition, the adaptive evolutionary mechanisms of the black wolfberry <italic>Fd-GOGAT</italic> gene were explored. The results showed that the genomes or transcriptomes of <italic>Lycium</italic> species contain two to four <italic>GS</italic> genes, two <italic>GOGAT</italic> genes, and three to four <italic>GDH</italic> genes. Following NaCl stress, the expression of <italic>Fd-GOGAT</italic> and <italic>NADH-GOGAT</italic> in the leaves of black wolfberry was downregulated with increasing time and NaCl concentration; in the roots, <italic>Fd-GOGAT</italic> and <italic>NADH-GOGAT</italic> were upregulated by 1.79-fold and 1.40-fold, respectively, 12 h after severe NaCl stress. <italic>GS2</italic> and <italic>GS1.1</italic> are highly expressed in leaves and roots, respectively, and their expression is significantly upregulated under NaCl stress. The expression of <italic>GDH</italic> in leaves is downregulated under salt stress, whereas in roots, the expression of <italic>NADP-GDH</italic> and <italic>GDH2</italic> is upregulated under NaCl stress. <italic>C2H2-63</italic>, a key transcription factor regulating nitrogen assimilation in black wolfberry under salt stress, is likely to promote nitrogen assimilation through its upregulated expression. Additionally, seven positively selected sites (p.Glu220, p.Ala388, p.Ala880, p.Ser921, p.Leu1319, p.Ser1350, and p.Ser1570) were found in the<italic> Fd-GOGAT</italic> protein of black wolfberry. Compared to Ningxia wolfberry (<italic>L. barbarum</italic>), these mutation sites enhance the affinity of <italic>Fd-GOGAT</italic> for its substrate Glu, which helps to increase the catalytic efficiency of <italic>Fd-GOGAT</italic> in black wolfberry under salt stress. In conclusion, the adaptation of salt stress-related nitrogen assimilation genes in black wolfberry involves both gene expression regulation and adaptive evolution. Enhancing the GS/GOGAT pathway under salt stress is a primary strategic choice for nitrogen assimilation in black wolfberry.