Transcriptomic and metabolomic analyses reveal the altitude adaptability and evolution of different colored flowers in alpine Rhododendron species.

Understanding the molecular mechanisms and evolutionary process of plant adaptation to heterogeneous environment caused by altitude gradients in plateau mountain ecosystems can provide novel insight into species response to global changes. Flower color is the most conspicuous and highly diverse traits in nature. Herein, the gene expression patterns, evolutionary adaptation, and the metabolites changes of different colored flowers of alpine Rhododendron species along altitude gradients were investigated based on a combined analysis of transcriptomics and metabolomics. Differentially expressed genes were found to be related to the biosynthesis of carbohydrates, fatty acids, amino acids, and flavonoids, suggesting their important roles in the altitude adaptability of Rhododendron species. The evolution rate of high-altitude species was faster than that of low-altitude species. Genes related to DNA repair, MAPK and ABA signal transduction, and lipoic acid and propanoate metabolism were positively selected in the flowers of high-altitude Rhododendron species and those associated with carotenoid biosynthesis pathway, ABA signal transduction, and ethylene signal transduction were positively selected in low-altitude species. These results indicated that the genes with differentiated expressions or functions exhibit varying evolutions during the adaptive divergence of heterogeneous environment caused by altitude gradients. Flower color variation might be attributed to the significant differences in gene expression or metabolites related to sucrose, flavonoids, and carotenoids at the transcription or metabolism levels of Rhododendron species. This work suggests that Rhododendron species have multiple molecular mechanisms in their adaptation to changing environments caused by altitude gradients.