Response of blade in Zanthoxylum planispinum var. Dintanensis to differences altitudes through integrated metabolomics and transcriptomics analysis

•The integrated analysis of metabolome and transcriptome in Z. planispinum var. Dintanensisin grown at different altitude are first reported within this study.•The altitude significantly affects the gene expression, and composition of secondary metabolites in leaves, and flavonoid metabolism may dominate the resistance of Zanthoxylum planispinum var. Dintanensis to the adverse environmental stress in rocky desertification control areas.•More flavonoids and phenolic acids were accumulated in higher altitudinal level, while more terpenoids, aldehyde and ester were distinctly increased in lower altitudinal level. Therefore, it is much more complicated to gain maximum medicinal productions of Z. planispinum var. Dintanensis.