Abstract Environmental factors such as altitude may significantly influence both the morphological trait and accumulation of metabolite products in plant. In present study, gene expression profiles of Z. planispinum var. Dintanensisin grown at different altitude (A1:1054 m.a.s.l., A2:821 m.a.s.l., A3:645 m.a.s.l.) were generated by using RNA-Seq. Four main medicinal ingredients of peels were determined, including the total acylamide, total flavonoids, total alkaloids and volatile oil content. The results showed that a total of 10,703 differentially expressed genes (DEGs) were identified among the three samples (A1, A2, A3), of these, 315 DEGs were putative transcription factors (TFs) belonging to 74 TF families. In particular, some candidate genes related to accumulation of main medicinal ingredients have been screened through combining Kmeans cluster and KEGG enrichment analysis. Besides, the total flavonoid accumulation exhibited a positive correlation with increasing altitude, suggesting that higher altitudes favor metabolite accumulation. Notably, seven genes and one MYB TF involved in the biosynthesis of the main medicinal ingredients were confirmed through RT-qPCR analysis The data obtained in this study offers a global survey of gene expression patterns of Z. planispinum var. Dintanensis grown in rocky desertification control areas, which support for further research on the high-altitude adaptation mechanism and identification of peels with higher medicinal value.
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