The origins of cultivated chrysanthemums have attracted considerable attention, but they remain poorly known. Here, we reconstructed the phylogeny of representative well-known cultivars and wild species of the genus Chrysanthemum using chloroplast genomes and the nuclear LEAFY gene. Our results suggest that geographic and ecological factors may determine the opportunities for wild species to be involved in the origin of the cultivars. The wild species C. indicum, C. zawadskii, C. dichrum, C. nankingense, C. argyrophyllum, and C. vestitum were likely directly or indirectly involved as paternal species of most of the chrysanthemum cultivars examined in this study. Yet, the maternal species is supported to be a lineage of an extinct wild Chrysanthemum species and its subsequent cultivars, as all accessions of chrysanthemum cultivars sampled formed a strongly supported clade, distinct from all other species of Chrysanthemum in the plastome tree. Thus, the cultivated chrysanthemums originated from multiple hybridizations involving several paternal species rather than only two or a few wild species, with an extinct species and its subsequent cultivars serving as the maternal parents. This finding is consistent with Chrysanthemum having high rates of hybridization and gene flow, which has been demonstrated within previous studies; nevertheless, it is important to unravel the role of an extinct wild Chrysanthemum species as the ultimate maternal parent species for all the chrysanthemum cultivars. Our results also suggest that C. vestitum from Tianzhu and Funiu Mountains in Anhui and Henan Provinces of China represent two distinct cryptic species.

Chrysanthemum rhombifolium (Ling et C. Shih), an endemic plant that is extremely well-adapted to harsh environments. However, little is known about its molecular biology of the plant's resistant traits against stress, or even its molecular biology of overall plant. To investigate the molecular biology of C. rhombifolium and mechanism of stress adaptation, we performed transcriptome sequencing of its leaves using an Illumina platform. A total of 130,891 unigenes were obtained, and 97,496 (~74.5%) unigenes were annotated in the public protein database. The similarity search indicated that 40,878 and 74,084 unigenes showed significant similarities to known proteins from NCBI non-redundant and Swissprot protein databases, respectively. Of these, 56,213 and 42,005 unigenes were assigned to the Gene Ontology (GO) database and Cluster of Orthologous Groups (COG), respectively, and 38,918 unigenes were mapped into five main categories, including 18 KEGG pathways. Metabolism was the largest category (23,128, 59.4%) among the main KEGG categories, suggesting active metabolic processes in C. rhombifolium. About 2,459 unigenes were annotated to have a role in defense mechanism or stress tolerance. Transcriptome analysis of C. rhombifolium revealed the presence of 12,925 microsatellites in 10,524 unigenes and mono, trip, and dinucleotides having higher polymorphism rates. The phylogenetic analysis based on GME gene among related species confirmed the reliability of the transcriptomic data. This work is the first genetic study of C. rhombifolium as a new plant resource of stress-tolerant genes. This large number of transcriptome sequences enabled us to comprehensively understand the basic genetics of C. rhombifolium and discover novel genes that will be helpful in the molecular improvement of chrysanthemums.

Introduction Chrysanthemums are traditional flowers that originated in China and have high ornamental, economic and medicinal value. They are widely used as herbal remedies and consumed as food or beverages in folk medicine. However, little is known about their metabolic composition. Objectives The aims of this work were to determine the metabolic composition of and natural variation among different species of Chrysanthemum and to explore new potential resources for drug discovery and sustainable utilisation of wild Chrysanthemum. Methods The metabolomes of Chrysanthemum mongolicum (Ling) Tzvel. and Chrysanthemum rhombifolium H. Ohashi & Yonek. were compared using a widely targeted metabolomics approach based on liquid chromatography–tandem mass spectrometry (LC–MS/MS). Results In total, 477 metabolites were identified, of which 72 showed significant differences in expression between C. mongolicum and C. rhombifolium, mainly in flavonoids, organic acids and nucleotides. The flavone and flavonol biosynthesis pathway showed significant enrichment among the differentially expressed metabolites. The contents of genkwanin, trigonelline, diosmin, narcissoside, 3,4‐dihydroxyphenylacetic acid, linarin, N′,N′‐p‐coumarin, C‐hexosyl‐tricetin O‐pentoside, chrysoeriol, acacetin and kaempferol‐3‐O‐gentiobioside were significantly different between the two species and represent potential biomarkers. Conclusion The types of flavonoid‐related metabolites in the flavonoid biosynthesis pathway differed between C. mongolicum and C. rhombifolium. The mechanisms underlying the unique adaptations of these two species to their environments may involve variations in the composition and abundance of flavonoids, organic acids, and nucleotides. These methods are promising to identify functional compounds in Chrysanthemum species and can provide potential resources for drug discovery and the sustainable utilisation of Chrysanthemum plants.