| Summary: | <i>Chrysanthemum mongolicum</i> and <i>Chrysanthemum vestitum</i> belong to the Asteraceae family, which occupy a wider range of ecological niches and represent extensive biotic resistance and abiotic tolerance. However, the genetic information about these two species is poorly known, which restricts their utilization. Here, the leaf transcriptomes of the two <i>Chrysanthemum</i> species were investigated and compared. In total, 21,856 differentially expressed genes (DEGs) were identified between <i>C. vestitum</i> and <i>C. mongolicum</i>, of which 12,076 DEGs were up-regulated and 9780 were down regulated in <i>C. vestitum</i> compared to <i>C. mongolicum</i>. Functional enrichment analysis revealed that stress resistance categories had significant proportions. The up-regulated DEGs related to “ABC transporters”, “Flavonoid biosynthesis” and “Monoterpenoid biosynthesis” were significantly enriched in <i>C. vestitum</i> compared with <i>C. mongolicum</i>. While the DEGs involved in “Biosynthesis of unsaturated fatty acids”, “Proteasome”, “Phenylpropanoid biosynthesis”, “Oxidative phosphorylation”, “Plant-pathogen interaction”, “Starch and sucrose metabolism”, “Glutathione metabolism”, as well as “MAPK signaling pathway” were mostly up-regulated in <i>C. mongolicum</i> compared with <i>C. vestitum</i>, suggesting their important roles in <i>C. mongolicum</i>. These results might explain the differences in morphology and provide potential molecular mechanisms for the ecological adaptation of the two <i>Chrysanthemum</i> species in extreme environments. Together, the results of this study provide a genetic resource that may greatly benefit the genetic improvement of cultivated chrysanthemums and will be helpful for plant conservation and sustainable utilization in the future.
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