Integrated physiological and transcriptomic analysis reveals molecular distinctions between Huanglongbing- and Zn/Mn deficiency-induced chlorosis in citrus

Background Citrus Huanglongbing (HLB) and zinc/manganese (Zn/Mn) deficiency induce similar chlorosis in young leaves, complicating field diagnosis. Despite visual similarities, the molecular mechanisms distinguishing these disorders remain unclear. This study employed integrated transcriptomic and physiological analyses to contrast HLB-specific responses with nutrient deficiency in Citrus sinensis (sweet orange) and Citrus reticulata 'Orah', aiming to identify the abiotic cause of chlorosis and clarify the underlying molecular divergence. Result “ Candidatus Liberibacter asiaticus” (CLas)-infected leaves showed significant downregulation of photosynthesis-related genes but upregulated starch/sucrose metabolism and phenylpropanoid biosynthesis, divergent from Zn/Mn-deficient leaves. Intriguingly, photosynthetic efficiency was independent of chlorosis severity. Starch accumulation was markedly higher and more consistent in HLB than in nutrient deficiency, serving as a predominant diagnostic marker. Flavonoid biosynthesis was significantly enhanced under both stresses, but the transcriptional induction was more pronounced and conserved across leaf positions in HLB. Additionally, plant-pathogen interaction pathways were activated exclusively in CLas-infected leaves, highlighting biotic stress-specific responses. Conclusion We propose a practical diagnostic matrix—pairing starch assays with molecular signatures of biotic defense—to differentiate HLB from nutrient deficiency. Our comparative analysis reveals HLB establishes a unique "defense-priority" metabolic state, offering both actionable management tools and a novel conceptual framework for understanding its pathology.