Integrative transcriptomic and metabolomic analyses of the drought response mechanisms of stem spines in desert plants from the Ebinur Lake.

Stem spines are key adaptive organs in desert plants, playing a critical role in resisting drought stress and maintaining plant survival. However, the molecular mechanisms governing their responses to drought remain insufficiently characterized. We investigated the stem spines of two representative halophytic shrubs from the Ebinur Lake Wetland desert region, Alhagi sparsifolia and Nitraria tangutorum, under a natural drought gradient: mild drought (Mi), 15.51% ± 0.61%; moderate drought (Mo), 8.87% ± 0.77%; severe drought (S), 3.34% ± 0.26%), and integrated transcriptomic and metabolomic analyses were performed to systematically reveal the molecular basis of stem spine responses to drought stress. The results showed that, compared with Mi, chlorophyll content in N. tangutorum stem spines decreased by 1.22- and 1.67-fold under Mo and S, respectively, whereas superoxide dismutase activity increased by 1.10-fold under Mo. Integrated transcriptome and metabolome analyses revealed that drought-responsive genes and metabolites under Mo and S were predominantly enriched in the isoflavonoid biosynthesis, arachidonic acid metabolism, steroid/brassinosteroid biosynthesis, and tryptophan metabolism pathways. In the tryptophan metabolism pathway, both metabolites and genes in N. tangutorum changed significantly, and tryptamine, auxin (IAA), and serotonin accumulated markedly under both Mo and S. In the isoflavonoid biosynthesis pathway, N. tangutorum exhibited increased genistein under Mo and elevated isoformononetin under S, whereas A. sparsifolia showed sustained accumulation of coumestrol and glyceollin II, with particularly strong increases in glyceollin II under both drought levels. This study revealed the molecular basis of drought responses in desert plant stem spines and offers insights into desert plant adaptation and ecosystem conservation strategies.