Phylogeny of the genus Chrysanthemum L.: evidence from single-copy nuclear gene and chloroplast DNA sequences

The haplotype-resolved genome of diploid Chrysanthemum indicum unveils new acacetin synthases genes and their evolutionary history

Acacetin, a flavonoid compound, possesses a wide range of pharmacological effects, including antimicrobial, immune regulation, and anticancer effects. Some key steps in its biosynthetic pathway were largely unknown in flowering plants. Here, we present the first haplotype-resolved genome of Chrysanthemum indicum, whose dried flowers contain abundant flavonoids and have been utilized as traditional Chinese medicine. Various phylogenetic analyses revealed almost equal proportion of three tree topologies among three Chrysanthemum species (C. indicum, C. nankingense, and C. lavandulifolium), indicating that frequent gene flow among Chrysanthemum species or incomplete lineage sorting due to rapid speciation might contribute to conflict topologies. The expanded gene families in C. indicum were associated with oxidative functions. Through comprehensive candidate gene screening, we identified five flavonoid O-methyltransferase (FOMT) candidates, which were highly expressed in flowers and whose expressional levels were significantly correlated with the content of acacetin. Further experiments validated two FOMTs (CI02A009970 and CI03A006662) were capable of catalyzing the conversion of apigenin into acacetin, and these two genes are possibly responsible acacetin accumulation in disc florets and young leaves, respectively. Furthermore, combined analyses of ancestral chromosome reconstruction and phylogenetic trees revealed the distinct evolutionary fates of the two validated FOMT genes. Our study provides new insights into the biosynthetic pathway of flavonoid compounds in the Asteraceae family and offers a model for tracing the origin and evolutionary routes of single genes. These findings will facilitate in vitro biosynthetic production of flavonoid compounds through cellular and metabolic engineering and expedite molecular breeding of C. indicum cultivars.

The use of an integrated framework combining eco-evolutionary data and species distribution models to predict range shifts of species under changing climates

Species distribution models (SDMs) are powerful tools that can predict potential distributions of species under climate change. However, traditional SDMs that rely on current species occurrences may underestimate their climatic tolerances and potential distributions. To address this limitation, we developed an integrated framework that incorporates eco-evolutionary data into SDMs. In our approach, the fundamental niches of species are constructed by their realized niches in different periods, and those fundamental niches are used to predict potential distributions of species. Our framework includes multiple phylogenetic analyses, such as niche evolution rate estimation and ancestral area reconstruction. These analyses provide deeper insights into the responses of species to climate change. We applied our approach to the Chrysanthemum zawadskii species complex to evaluate its efficacy through comprehensive performance evaluations and validation tests. Our framework can be applied broadly to species with available phylogenetic data and occurrence records, making it a valuable tool for understanding species adaptation in a rapidly changing world.•Integrating the niches of species in different periods estimates more complete climatic envelopes for them.•Combining eco-evolutionary data with SDMs predicts more comprehensive potential distributions of species under climate change.•Our framework provides a general procedure for species with phylogenetic data and occurrence records.

Genome-Wide Analysis of MYB Gene Family in Chrysanthemum ×morifolium Provides Insights into Flower Color Regulation

MYBs constitute the second largest transcription factor (TF) superfamily in flowering plants with substantial structural and functional diversity, which have been brought into focus because they affect flower colors by regulating anthocyanin biosynthesis. Up to now, the genomic data of several Chrysanthemum species have been released, which provides us with abundant genomic resources for revealing the evolution of the MYB gene family in Chrysanthemum species. In the present study, comparative analyses of the MYB gene family in six representative species, including C. lavandulifolium, C. seticuspe, C. ×morifolium, Helianthus annuus, Lactuca sativa, and Arabidopsis thaliana, were performed. A total of 1104 MYBs, which were classified into four subfamilies and 35 lineages, were identified in the three Chrysanthemum species (C. lavandulifolium, C. seticuspe, and C. ×morifolium). We found that whole-genome duplication and tandem duplication are the main duplication mechanisms that drove the occurrence of duplicates in CmMYBs (particularly in the R2R3-MYB subfamily) during the evolution of the cultivated chrysanthemums. Sequence structure and selective pressure analyses of the MYB gene family revealed that some of R2R3-MYBs were subjected to positive selection, which are mostly located on the distal telomere segments of the chromosomes and contain motifs 7 and 8. In addition, the gene expression analysis of CmMYBs in different organs and at various capitulum developmental stages of C. ×morifolium indicated that CmMYBS2, CmMYB96, and CmMYB109 might be the negative regulators for anthocyanin biosynthesis. Our results provide the phylogenetic context for research on the genetic and functional evolution of the MYB gene family in Chrysanthemum species and deepen our understanding of the regulatory mechanism of MYB TFs on the flower color of C. ×morifolium.

Comparative transcriptome analysis provides molecular insights into heterosis of waterlogging tolerance in Chrysanthemum indicum

BACKGROUND

Heterosis breeding is one of the most important breeding methods for chrysanthemum. To date, the genetic mechanisms of heterosis for waterlogging tolerance in chrysanthemum are still unclear. This study aims to analyze the expression profiles and potential heterosis-related genes of two hybrid lines and their parents with extreme differences in waterlogging tolerance under control and waterlogging stress conditions by RNA-seq.

RESULTS

A population of 140 F1 progeny derived from Chrysanthemum indicum (Nanchang) (waterlogging-tolerant) and Chrysanthemum indicum (Nanjing) (waterlogging-sensitive) was used to characterize the extent of genetic variation in terms of seven waterlogging tolerance-related traits across two years. Lines 98 and 95, respectively displaying positive and negative overdominance heterosis for the waterlogging tolerance traits together with their parents under control and waterlogging stress conditions, were used for RNA-seq. In consequence, the maximal number of differentially expressed genes (DEGs) occurred in line 98. Gene ontology (GO) enrichment analysis revealed multiple stress-related biological processes for the common up-regulated genes. Line 98 had a significant increase in non-additive genes under waterlogging stress, with transgressive up-regulation and paternal-expression dominant patterns being the major gene expression profiles. Further, GO analysis identified 55 and 95 transgressive up-regulation genes that overlapped with the up-regulated genes shared by two parents in terms of responses to stress and stimulus, respectively. 6,640 genes in total displaying maternal-expression dominance patterns were observed in line 95. In addition, 16 key candidate genes, including SAP12, DOX1, and ERF017 which might be of significant importance for the formation of waterlogging tolerance heterosis in line 98, were highlighted.

CONCLUSION

The current study provides a comprehensive overview of the root transcriptomes among F1 hybrids and their parents under waterlogging stress. These findings lay the foundation for further studies on molecular mechanisms underlying chrysanthemum heterosis on waterlogging tolerance.

Structural divergence and phylogenetic relationships of Ajania (Asteraceae) from plastomes and ETS

BACKGROUND

Ajania Poljakov, an Asteraceae family member, grows mostly in Asia's arid and semi-desert areas and is a significant commercial and decorative plant. Nevertheless, the genus' classification has been disputed, and the evolutionary connections within the genus have not been thoroughly defined. Hence, we sequenced and analyzed Ajania's plastid genomes and combined them with ETS data to assess their phylogenetic relationships.

RESULTS

We obtained a total of six new Ajania plastid genomes and nine ETS sequences. The whole plastome lengths of the six species sampled ranged from 151,002 bp to 151,115 bp, showing conserved structures. Combined with publicly available data from GenBank, we constructed six datasets to reconstruct the phylogenetic relationships, detecting nucleoplasmic clashes. Our results reveal the affinities of Artemisia, Chrysanthemum and Stilpnolepis to Ajania and validate the early taxonomy reclassification. Some of the plastid genes with low phylogenetic information and gene trees with topological differences may have contributed to the ambiguous phylogenetic results of Ajania. There is extensive evolutionary rate heterogeneity in plastid genes. The psbH and ycf2 genes, which are involved in photosynthesis and ATP transport, are under selective pressure. Plastomes from Ajania species diverged, and structural aspects of plastomes may indicate some of the real evolutionary connections. We suggest the ycf1 gene as a viable plastid DNA barcode because it has significant nucleotide diversity and better reflects evolutionary connections.

CONCLUSION

Our findings validate the early Ajania taxonomy reclassification and show evolutionary rate heterogeneity, genetic variety, and phylogenetic heterogeneity of plastid genes. This research might provide new insights into the taxonomy and evolution of Ajania, as well as provide useful information for germplasm innovation and genetic enhancement in horticultural species.

Current Achievements and Future Prospects in Virus Elimination Technology for Functional Chrysanthemum

Chrysanthemum is an important functional plant that is used for food, medicine and tea. Functional chrysanthemums become infected with viruses all around the world, seriously lowering their quality and yield. Viral infection has become an important limiting factor in chrysanthemum production. Functional chrysanthemum is often propagated asexually by cutting during production, and viral infection of seedlings is becoming increasingly serious. Chrysanthemums can be infected by a variety of viruses causing different symptoms. With the development of biotechnology, virus detection and virus-free technologies for chrysanthemum seedlings are becoming increasingly effective. In this study, the common virus species, virus detection methods and virus-free technology of chrysanthemum infection are reviewed to provide a theoretical basis for virus prevention, treatment and elimination in functional chrysanthemum.

Analyses of a chromosome-scale genome assembly reveal the origin and evolution of cultivated chrysanthemum

Chrysanthemum (Chrysanthemum morifolium Ramat.) is a globally important ornamental plant with great economic, cultural, and symbolic value. However, research on chrysanthemum is challenging due to its complex genetic background. Here, we report a near-complete assembly and annotation for C. morifolium comprising 27 pseudochromosomes (8.15 Gb; scaffold N50 of 303.69 Mb). Comparative and evolutionary analyses reveal a whole-genome triplication (WGT) event shared by Chrysanthemum species approximately 6 million years ago (Mya) and the possible lineage-specific polyploidization of C. morifolium approximately 3 Mya. Multilevel evidence suggests that C. morifolium is likely a segmental allopolyploid. Furthermore, a combination of genomics and transcriptomics approaches demonstrate the C. morifolium genome can be used to identify genes underlying key ornamental traits. Phylogenetic analysis of CmCCD4a traces the flower colour breeding history of cultivated chrysanthemum. Genomic resources generated from this study could help to accelerate chrysanthemum genetic improvement.

Hyb-Seq provides new insights into the phylogeny and evolution of the Chrysanthemum zawadskii species complex in China

A species complex is an assemblage of closely related species with blurred boundaries, and from which species could arise from different speciation processes and/or a speciation continuum. Such a complex can provide an opportunity to investigate evolutionary mechanisms acting on speciation. The Chrysanthemum zawadskii species complex in China, a monophyletic group of Chrysanthemum, consists of seven species with considerable morphological variation, diverse habitats and different distribution patterns. Here, we used Hyb-Seq data to construct a well-resolved phylogeny of the C. zawadskii complex. Then, we performed comparative analyses of variation patterns in morphology, ecology and distribution to investigate the roles of geography and ecology in this complex's diversification. Lastly, we implemented divergence time estimation, species distribution modelling and ancestral area reconstruction to trace the evolutionary history of this complex. We concluded that the C. zawadskii complex originated in the Qinling-Daba mountains during the early Pliocene and then spread west and northward along the mountain ranges to northern China. During this process, geographical and ecological factors imposing different influences resulted in the current diversification and distribution patterns of this species complex, which is composed of both well-diverged species and diverging lineages on the path of speciation.

Rhamnosyltransferases involved in the biosynthesis of flavone rutinosides in Chrysanthemum species

Linarin (acacetin-7-O-rutinoside), isorhoifolin (apigenin-7-O-rutinoside), and diosmin (diosmetin-7-O-rutinoside) are chemically and structurally similar flavone rutinoside (FR) compounds found in Chrysanthemum L. (Anthemideae, Asteraceae) plants. However, their biosynthetic pathways remain largely unknown. In this study, we cloned and compared FRs and genes encoding rhamnosyltransferases (RhaTs) among eight accessions of Chrysanthemum polyploids. We also biochemically characterized RhaTs of Chrysanthemum plants and Citrus (Citrus sinensis and Citrus maxima). RhaTs from these two genera are substrate-promiscuous enzymes catalyzing the rhamnosylation of flavones, flavanones, and flavonols. Substrate specificity analysis revealed that Chrysanthemum 1,6RhaTs preferred flavone glucosides (e.g. acacetin-7-O-glucoside), whereas Cs1,6RhaT preferred flavanone glucosides. The nonsynonymous substitutions of RhaTs found in some cytotypes of diploids resulted in the loss of catalytic function. Phylogenetic analysis and specialized pathways responsible for the biosynthesis of major flavonoids in Chrysanthemum and Citrus revealed that rhamnosylation activity might share a common evolutionary origin. Overexpression of RhaT in hairy roots resulted in 13-, 2-, and 5-fold increases in linarin, isorhoifolin, and diosmin contents, respectively, indicating that RhaT is mainly involved in the biosynthesis of linarin. Our findings not only suggest that the substrate promiscuity of RhaTs contributes to the diversity of FRs in Chrysanthemum species but also shed light on the evolution of flavone and flavanone rutinosides in distant taxa.

Co-option of a carotenoid cleavage dioxygenase gene (CCD4a) into the floral symmetry gene regulatory network contributes to the polymorphic floral shape-color combinations in Chrysanthemum sensu lato

Morphological novelties, including formation of trait combinations, may result from de novo gene origination and/or co-option of existing genes into other developmental contexts. A variety of shape-color combinations of capitular florets occur in Chrysanthemum and its allies. We hypothesized that co-option of a carotenoid cleavage dioxygenase gene into the floral symmetry gene network would generate a white zygomorphic ray floret. We tested this hypothesis in an evolutionary context using species in Chrysanthemum sensu lato, a monophyletic group with diverse floral shape-color combinations, based on morphological investigation, interspecific crossing, molecular interaction and transgenic experiments. Our results showed that white color was significantly associated with floret zygomorphy. Specific expression of the carotenoid cleavage dioxygenase gene CCD4a in marginal florets resulted in white color. Crossing experiments between Chrysanthemum lavandulifolium and Ajania pacifica indicated that expression of CCD4a is trans-regulated. The floral symmetry regulator CYC2g can activate expression of CCD4a with a dependence on TEOSINTE BRANCHED1/CYCLOIDEA/PROLIFERATING (TCP) binding element 8 on the CCD4a promoter. Based on all experimental findings, we propose that gene co-option of carotenoid degradation into floral symmetry regulation, and the subsequent dysfunction or loss of either CYC2g or CCD4a, may have led to evolution of capitular shape-color patterning in Chrysanthemum sensu lato.

Towards the Improvement of Ornamental Attributes in Chrysanthemum: Recent Progress in Biotechnological Advances

Incessant development and introduction of novel cultivars with improved floral attributes are vital in the dynamic ornamental industry. Chrysanthemum (Chrysanthemum morifolium) is a highly favored ornamental plant, ranking second globally in the cut flower trade, after rose. Development of new chrysanthemum cultivars with improved and innovative modifications in ornamental attributes, including floral color, shape, plant architecture, flowering time, enhanced shelf life, and biotic and abiotic stress tolerance, is a major goal in chrysanthemum breeding. Despite being an economically important ornamental plant, the application of conventional and molecular breeding approaches to various key traits of chrysanthemum is hindered owing to its genomic complexity, heterozygosity, and limited gene pool availability. Although classical breeding of chrysanthemum has resulted in the development of several hundreds of cultivars with various morphological variations, the genetic and transcriptional control of various important ornamental traits remains unclear. The coveted blue colored flowers of chrysanthemums cannot be achieved through conventional breeding and mutation breeding due to technical limitations. However, blue-hued flower has been developed by genetic engineering, and transgenic molecular breeding has been successfully employed, leading to substantial progress in improving various traits. The recent availability of whole-genome sequences of chrysanthemum offers a platform to extensively employ MAS to identify a large number of markers for QTL mapping, and GWAS to dissect the genetic control of complex traits. The combination of NGS, multi-omic platforms, and genome editing technologies has provided a tremendous scope to decipher the molecular and regulatory mechanisms. However, the application and integration of these technologies remain inadequate for chrysanthemum. This review, therefore, details the significance of floral attributes, describes the efforts of recent advancements, and highlights the possibilities for future application towards the improvement of crucial ornamental traits in the globally popular chrysanthemum plant.

The genus Chrysanthemum: Phylogeny, biodiversity, phytometabolites, and chemodiversity

The ecologically and economically important genus Chrysanthemum contains around 40 species and many hybrids and cultivars. The dried capitulum of Chrysanthemum morifolium (CM) Ramat. Tzvel, i.e., Flos Chrysanthemi, is frequently used in traditional Chinese medicine (TCM) and folk medicine for at least 2,200 years. It has also been a popular tea beverage for about 2,000 years since Han Dynasty in China. However, the origin of different cultivars of CM and the phylogenetic relationship between Chrysanthemum and related Asteraceae genera are still elusive, and there is a lack of comprehensive review about the association between biodiversity and chemodiversity of Chrysanthemum. This article aims to provide a synthetic summary of the phylogeny, biodiversity, phytometabolites and chemodiversity of Chrysanthemum and related taxonomic groups, focusing on CM and its wild relatives. Based on extensive literature review and in light of the medicinal value of chrysanthemum, we give some suggestions for its relationship with some genera/species and future applications. Mining chemodiversity from biodiversity of Chrysanthemum containing subtribe Artemisiinae, as well as mining therapeutic efficacy and other utilities from chemodiversity/biodiversity, is closely related with sustainable conservation and utilization of Artemisiinae resources. There were eight main cultivars of Flos Chrysanthemi, i.e., Hangju, Boju, Gongju, Chuju, Huaiju, Jiju, Chuanju and Qiju, which differ in geographical origins and processing methods. Different CM cultivars originated from various hybridizations between multiple wild species. They mainly contained volatile oils, triterpenes, flavonoids, phenolic acids, polysaccharides, amino acids and other phytometabolites, which have the activities of antimicrobial, anti-viral, antioxidant, anti-aging, anticancer, anti-inflammatory, and closely related taxonomic groups could also be useful as food, medicine and tea. Despite some progresses, the genetic/chemical relationships among varieties, species and relevant genera have yet to be clarified; therefore, the roles of pharmacophylogeny and omics technology are highlighted.

Chrysanthemumdabieshanense, a new name for Chrysanthemumvestitum var. latifolium (Asteraceae, Anthemideae)

Recent phylogenetic analyses have revealed that Chrysanthemumvestitumvar.latifolium and C.vestitumvar.vestitum were placed in different clades based on their chloroplast genomes and nuclear LFAFY gene sequences. Accordingly, based on previous morphological analysis, molecular phylogenetic results, fieldwork, and herbarium studies, Chrysanthemumvestitumvar.latifolium should be raised to the species level. Considering the condition of the material found and Articles 6.9, 6.11, 41.2, 58.1 of the International Code of Nomenclature for Algae, Fungi, and Plants (Shenzhen Code) that is currently in force, Chrysanthemumdabieshanense Z.X.Fu, A.G.Zhen, & Y.P.Ma, nom. nov. is proposed as the new name for Chrysanthemumvestitumvar.latifolium J.Zhou & Jun Y.Chen. The detailed emended description, distribution map, insights into its habitat, and an updated comparative morphological study are presented in this study.

Taxonomic delimitation and molecular identification of clusters within the species Zanthoxylumnitidum (Rutaceae) in China

Zanthoxylumnitidum, known as Liang-Mian-Zhen in China, is a traditional Chinese medicinal plant used to treat traumatic injury, rheumatism, paralysis, toothache, stomach ache, and venomous snake bites. Two varieties of the species have been described and three morphological types have been reported within the original variety. However, taxonomic delimitation and molecular markers for distinguishing these varieties and types within this species remain unknown. Since different populations exhibit varying chemical compositions, easy identification of intraspecific taxa is crucial. We collected 420 individuals from 38 natural populations, 3 samples of standard medicinal material, and 17 folk-medicine samples to perform classification and identification within Zanthoxylumnitidum. Four distinct genetic clusters (A, B, C, and D) were highly supported by the nuclear barcode. Two distinct chloroplast clusters (A1 and A2) were further detected within A, and three others had one-to-one correspondence with the remaining nuclear clusters. Molecular identification showed that the 17 folk samples comprised A1, A2, B, and D, while the 3 standard samples belonged to A2. The internal transcribed spacer (ITS) region and rbcL gene are proposed as barcodes for rapid and accurate identification of the different Liang-Mian-Zhen lineages in China. This study highlights the importance of accurate taxonomic delimitation in combination with rapid and accurate molecular identification of medicinal plants.

Biogeographic and metabolic studies support a glacial radiation hypothesis during Chrysanthemum evolution

Chrysanthemum (Chrysanthemum morifolium Ramat.) is an economically important plant species growing worldwide. However, its origin, especially as revealed by biogeographic and metabolomics research, remains unclear. To understand the geographic distribution of species diversity and metabolomics in three genera (Chrysanthemum, Ajania, and Phaeostigma), geographic information systems and gas chromatography-mass spectrometry were used in 19, 15, and 4 species respectively. China and Japan were two potential panbiogeographic nodes and diverse hotspots of Chrysanthemum, with species richness ratios of 58.97 and 33.33%. We studied different species from two hotspots which in similar geographical environments had closer chemotaxonomic relationships under the same cultivation conditions based on a cluster of 30 secondary metabolites. The average distribution altitude (ADA) differed significantly among Chrysanthemum, Ajania, and Phaeostigma in which it was 1227.49, 2400.12, and 3760.53 m.a.s.l. respectively, and the presence/absence of ray florets (RF) was significantly correlated with ADA (-0.62). Mountain landform was an important contributor to global Chrysanthemum diversity, playing a key role in the divergence and distribution pattern of Chrysanthemum and its allies. The Hengduan Mountains-Qinling Mountains (HDQ) in China was a potential secondary radiation and evolution center of Chrysanthemum and its related genera in the world. During the Quaternary glacial-interglacial cycles, this region became their refuge, and they radiated and evolved from this center.

The complete sequence of the chloroplast genome of Chrysanthemum rupestre, a diploid disciform capitula species of Chrysanthemum

In this study, we analyzed the complete sequence of the chloroplast genome of Chrysanthemum rupestre Matsum. et Koidz., 1910, a diploid disciform capitula species of Chrysanthemum endemic to Japan, formerly classified as Ajania rupestris (Matsum. & Koidz.) Muldashev, Bot. Zhurn. (Moscow & Leningrad), 1983. The chloroplast genome of C. rupestre has a typical conserved quadripartite structure of 151,061 bp in length, comprising a large single-copy region (82,846 bp), a small single-copy region (18,301 bp), and a pair of inverted repeat regions (each 24,957 bp). Phylogenetic analysis indicated that C. rupestre clustered with other Chrysanthemum species, including another former Ajania species, Chrysanthemum pacificum Nakai, 1928. However, Ajania variifolia (C.C.Chang) Tzvelev, 1961, which is a synonym of Phaeostigma variifolium (C.C.Chang) Muldashev, 1981, was placed outside the Chrysanthemum clade, thereby implying that the former genus Ajania includes heterogeneous species.

De novo whole-genome assembly of Chrysanthemum makinoi, a key wild chrysanthemum

Chrysanthemum is among the top 10 cut, potted, and perennial garden flowers in the world. Despite this, to date, only the genomes of two wild diploid chrysanthemums have been sequenced and assembled. Here, we present the most complete and contiguous chrysanthemum de novo assembly published so far, as well as a corresponding ab initio annotation. The cultivated hexaploid varieties are thought to originate from a hybrid of wild chrysanthemums, among which the diploid Chrysanthemum makinoi has been mentioned. Using a combination of Oxford Nanopore long reads, Pacific Biosciences long reads, Illumina short reads, Dovetail sequences, and a genetic map, we assembled 3.1 Gb of its sequence into nine pseudochromosomes, with an N50 of 330 Mb and a BUSCO complete score of 92.1%. Our ab initio annotation pipeline predicted 95,074 genes and marked 80.0% of the genome as repetitive. This genome assembly of C. makinoi provides an important step forward in understanding the chrysanthemum genome, evolution, and history.

The Maternal Donor of Chrysanthemum Cultivars Revealed by Comparative Analysis of the Chloroplast Genome

Chrysanthemum (Chrysanthemum morifolium Ramat) is an important floricultural crop and medicinal herb. Modern chrysanthemum cultivars have complex genetic backgrounds because of multiple cycles of hybridization, polyploidization, and prolonged cultivation. Understanding the genetic background and hybrid origin of modern chrysanthemum cultivars can provide pivotal information for chrysanthemum genetic improvement and breeding. By now, the origin of cultivated chrysanthemums remains unclear. In this study, 36 common chrysanthemum cultivars from across the world and multiple wild relatives were studied to identify the maternal donor of modern chrysanthemum. Chloroplast (cp) genomes of chrysanthemum cultivars were assembled and compared with those of the wild relatives. The structure of cp genomes was highly conserved among cultivars and wild relatives. Phylogenetic analyses based on the assembled cp genomes showed that all chrysanthemum cultivars grouped together and shared 64 substitutions that were distinct from those of their wild relatives. These results indicated that a diverged lineage of the genus Chrysanthemum, which was most likely an extinct or un-sampled species/population, provided a maternal source for modern cultivars. These findings provide important insights into the origin of chrysanthemum cultivars, and a source of valuable genetic markers for chrysanthemum breeding programs.

A chromosome-level genome sequence of Chrysanthemum seticuspe, a model species for hexaploid cultivated chrysanthemum

Chrysanthemums are one of the most industrially important cut flowers worldwide. However, their segmental allopolyploidy and self-incompatibility have prevented the application of genetic analysis and modern breeding strategies. We thus developed a model strain, Gojo-0 (Chrysanthemum seticuspe), which is a diploid and self-compatible pure line. Here, we present the 3.05 Gb chromosome-level reference genome sequence, which covered 97% of the C. seticuspe genome. The genome contained more than 80% interspersed repeats, of which retrotransposons accounted for 72%. We identified recent segmental duplication and retrotransposon expansion in C. seticuspe, contributing to arelatively large genome size. Furthermore, we identified a retrotransposon family, SbdRT, which was enriched in gene-dense genome regions and had experienced a very recent transposition burst. We also demonstrated that the chromosome-level genome sequence facilitates positional cloning in C. seticuspe. The genome sequence obtained here can greatly contribute as a reference for chrysanthemum in front-line breeding including genome editing.

The complete chloroplast genome of Chrysanthemum zawadskii Herbich (Asteraceae) isolated in Korea

We have determined the complete chloroplast genome of Chrysanthemum zawadskii Herbich isolated in Korea. The circular chloroplast genome of C. zawadskii is 151,137 bp long and has four subregions: 83,041 bp of large single copy and 18,350 bp of small single copy regions are separated by 24,873 bp of inverted repeat regions including 133 genes (87 protein-coding genes, eight rRNA genes, 37 tRNAs, and one pseudogene). There are 65 to 152 single nucleotide polymorphisms and 33 to 64 insertion and deletion regions (178 bp to 372 bp in length) identified against three available chloroplast genomes of C. zawadskii. The phylogenetic tree shows that C. zawadskii is clustered as a paraphyletic group with C. zawadskii subsp. coreanum, displaying incongruency between species and clades.

Clarifying Recent Adaptive Diversification of the Chrysanthemum-Group on the Basis of an Updated Multilocus Phylogeny of Subtribe Artemisiinae (Asteraceae: Anthemideae)

Understanding the roles played by geography and ecology in driving species diversification and in the maintenance of species cohesion is the central objective of evolutionary and ecological studies. The multi-phased orogenesis of Qinghai-Tibetan Plateau (QTP) and global climate changes over late-Miocene has profoundly influenced the environments and evolution of organisms in this region and the vast areas of Asia. In this study, we investigate the lineage diversification of Chrysanthemum-group in subtribe Artemisiinae (tribe Anthemideae, Asteraceae) likely under the effects of climate changes during this period. Using DNA sequences of seven low-copy nuclear loci and nrITS and the coalescent analytical methods, a time-calibrated phylogeny of subtribe Artemisiinae was reconstructed with emphasis on Chrysanthemum-group. The monophyletic Chrysanthemum-group was well resolved into two major clades corresponding to Chrysanthemum and Ajania, two genera which can be well identified by capitulum morphology but have been intermingled in previous plastid and ITS trees. Within Chrysanthemum, a later divergence between Ch. indicum-complex and Ch. zawadskii-complex can be recognized. The time frames of these sequential divergences coincide with the late Cenozoic uplift of the Northern QTP and the concomitant climatic heterogeneity between eastern and inland Asia. Reconstruction of historical biogeography suggested the origin of Chrysanthemum-group in Central Asia, followed by eastward migration of Chrysanthemum and in situ diversification of Ajania. Within Chrysanthemum, Ch. indicum-complex and Ch. zawadskii-complex exhibited contemporary distributional division, the former in more southern and the latter in more northern regions. The geographic structure of the three lineages in Chrysanthemum-group have been associated with the niche differentiation, and environmental heterogenization in Asia interior.

Chemistry and Pharmacological Activity of Sesquiterpenoids from the Chrysanthemum Genus

Plants from the Chrysanthemum genus are rich sources of chemical diversity and, in recent years, have been the focus of research on natural products chemistry. Sesquiterpenoids are one of the major classes of chemical constituents reported from this genus. To date, more than 135 sesquiterpenoids have been isolated and identified from the whole genus. These include 26 germacrane-type, 26 eudesmane-type, 64 guaianolide-type, 4 bisabolane-type, and 15 other-type sesquiterpenoids. Pharmacological studies have proven the biological potential of sesquiterpenoids isolated from Chrysanthemum species, reporting anti-inflammatory, antibacterial, antitumor, insecticidal, and antiviral activities for these interesting molecules. In this paper, we provide information on the chemistry and bioactivity of sesquiterpenoids obtained from the Chrysanthemum genus which could be used as the scientific basis for their future development and utilization.

Dysfunction of CYC2g is responsible for the evolutionary shift from radiate to disciform flowerheads in the Chrysanthemum group (Asteraceae: Anthemideae)

Evolutionary shifts among radiate, disciform and discoid flowerheads have occurred repeatedly in a number of major lineages across the Asteraceae phylogeny; such transitions may also appear within evolutionarily young groups. Although several studies have demonstrated that CYC2 genes partake in regulating floral morphogenesis in Asteraceae, the evolution of capitulum forms within a recently diverging lineage has remained poorly understood. Here, we study the molecular regulation of the shift from a radiate to a disciform capitulum within the Chrysanthemum group. This is a recently radiating group mainly comprising two genera, Chrysanthemum and Ajania, that are phylogenetically intermingled but distinct in flowerhead morphology: Chrysanthemum spp. with radiate capitula and Ajania spp. with disciform capitula. We found that the morphogenesis of zygomorphy in the marginal floret in Ajania was disrupted soon after floral primordium emergence; CYC2g, one of the CYC2 copies that was expressed prominently in the ray floret of Chrysanthemum was not expressed in flowerheads of Ajania. Weakening the expression of ClCYC2g in Chrysanthemum lavandulifolium led to the gradual transition of a ray flower toward the disc-like form. Molecular evolutionary analyses indicated that the disciform capitulum might have evolved only once, approximately 8 Mya, arising from dysfunction of the CYC2g orthologs. A 20-nt deletion, including a putative TATA-box of the Ajania-type CYC2g promoter, appeared to inhibit the expression of the gene. Considering the divergent habitats of Chrysanthemum and Ajania, we propose that the shift from radiate to disciform capitulum must have been related to changes in pollination strategies under selective pressure.

Small-scale alpine topography at low latitudes and high altitudes: refuge areas of the genus Chrysanthemum and its allies

Cultivated chrysanthemum (Chrysanthemum morifolium Ramat.) is an economically important ornamental plant species grown worldwide. However, the origin of the genus Chrysanthemum remains unclear. This study was conducted in the Hengduan Mountains, Yunnan Province. We took advantage of a special geographic region where the southernmost species of Ajania and the highest altitude population of Chrysanthemum indicum coexist to investigate their evolutionary origins. Diversity analysis of 9 populations of 5 species that came from 3 genera was carried out based on morphological traits and SRAP markers. Furthermore, topographical and ecological analyses and surveys of the vegetation communities in the plots were carried out for correlation analysis, and past data were used to reconstruct the ancient topography and vegetation to estimate the migration path and divergence time. We found that Chrysanthemum and Ajania were closely related based on the smooth transition states among marginal female florets and their common pollination system. The genetic relationship between Phaeostigma and Chrysanthemum was relatively distant, and Ajania was between them. Low light intensity and relatively humid habitats may be driving the elongation and evolution of marginal female florets. We found that Chrysanthemum and related genera were largely restricted to stony topographies at an altitude of ~3000 m.a.s.l. and in specialized alpine coniferous (Pinus) and broad-leaved (Quercus) mixed forest marginal communities. These stony topographies have become ecological islands of refuge for these species in the current interglacial period. The Hengduan Mountains play a key role in the evolution, divergence, and survival of Chrysanthemum and its allies.

The Evolution of Chromosome Numbers: Mechanistic Models and Experimental Approaches

Chromosome numbers have been widely used to describe the most fundamental genomic attribute of an organism or a lineage. Although providing strong phylogenetic signal, chromosome numbers vary remarkably among eukaryotes at all levels of taxonomic resolution. Changes in chromosome numbers regularly serve as indication of major genomic events, most notably polyploidy and dysploidy. Here, we review recent advancements in our ability to make inferences regarding historical events that led to alterations in the number of chromosomes of a lineage. We first describe the mechanistic processes underlying changes in chromosome numbers, focusing on structural chromosomal rearrangements. Then, we focus on experimental procedures, encompassing comparative cytogenomics and genomics approaches, and on computational methodologies that are based on explicit models of chromosome-number evolution. Together, these tools offer valuable predictions regarding historical events that have changed chromosome numbers and genome structures, as well as their phylogenetic and temporal placements.

Identification of the Volatile Compounds and Observation of the Glandular Trichomes in Opisthopappus taihangensis and Four Species of Chrysanthemum

Opisthopappus taihangensis (Ling) Shih, a wild relative germplasm of chrysanthemum, releases a completely different fragrance from chrysanthemum species. We aimed to identify the volatile compounds of the leaves of O. taihangensis and four other Chrysanthemum species using headspace solid-phase micro-extraction combined with gas chromatography-mass spectrometry (HS-SPME-GC/MS). In total, 70 compounds were detected, and terpenoids accounted for the largest percentage in these five species. Many specific compounds were only emitted from O. taihangensis and not from the other four species. In particular, 1,8-cineole could be responsible for the special leaf fragrance of O. taihangensis as it accounted for the largest proportion of the compounds in O. taihangensis but a small or no proportion at all in other species. The glandular trichomes (GTs) in the leaves are the main organs responsible for the emission of volatiles. To explore the relationship between the emissions and the density of the GTs on the leaf epidermis, the shape and density of the GTs were observed and calculated, respectively. The results showed that the trichomes have two shapes in these leaves: T-shaped non-glandular trichomes and capitate trichomes. Histochemical staining analyses indicated that terpenoids are mainly emitted from capitate glandular trichomes. Correlation analysis showed that the volatile amount of terpenoids is highly related to the density of capitate trichomes. In O. taihangensis, the terpenoids content and density of capitate trichomes are the highest. We identified the diversity of leaf volatiles from O. taihangensis and four other Chrysanthemum species and found a possible relationship between the content of volatile compounds and the density of capitate trichomes, which explained the cause of the fragrance of O. taihangensis leaves.

A comparative analysis of the complete chloroplast genomes of three Chrysanthemum boreale strains

BACKGROUND

Chrysanthemum boreale Makino (Anthemideae, Asteraceae) is a plant of economic, ornamental and medicinal importance. We characterized and compared the chloroplast genomes of three C. boreale strains. These were collected from different geographic regions of Korea and varied in floral morphology.

METHODS

The chloroplast genomes were obtained by next-generation sequencing techniques, assembled de novo, annotated, and compared with one another. Phylogenetic analysis placed them within the Anthemideae tribe.

RESULTS

The sizes of the complete chloroplast genomes of the C. boreale strains were 151,012 bp (strain 121002), 151,098 bp (strain IT232531) and 151,010 bp (strain IT301358). Each genome contained 80 unique protein-coding genes, 4 rRNA genes and 29 tRNA genes. Comparative analyses revealed a high degree of conservation in the overall sequence, gene content, gene order and GC content among the strains. We identified 298 single nucleotide polymorphisms (SNPs) and 106 insertions/deletions (indels) in the chloroplast genomes. These variations were more abundant in non-coding regions than in coding regions. Long dispersed repeats and simple sequence repeats were present in both coding and noncoding regions, with greater frequency in the latter. Regardless of their location, these repeats can be used for molecular marker development. Phylogenetic analysis revealed the evolutionary relationship of the species in the Anthemideae tribe. The three complete chloroplast genomes will be valuable genetic resources for studying the population genetics and evolutionary relationships of Asteraceae species.

The complete chloroplast genome sequence of Ajania pacifica (Nakai) Bremer & Humphries

The complete chloroplast (cp) genome sequence of Ajania pacifica, called as golden and silver chrysanthemum, was newly analyzed in this study. It was 151,059 bp in length and was a typical circular structure composed of and comprised of a large single copy region (82,857 bp) and a small single copy region (18,294 bp) which were separated by two inverted repeat regions (24,954 bp). The molecular phylogenetic analyses of A. pacifica and its related taxa was conducted based on the complete chloroplast genome sequences, and it was proved that the genus Ajania is embedded in the genus Chrysanthemum clade as well as a monotypic genus Opisthopappus. In the other hand, the genus Artemisia was divided into two group in the tribe Anthemideae.

Unraveling Natural Products' Role in Osteoarthritis Management-An Overview

The natural process of aging gradually causes changes in living organisms, leading to the deterioration of organs, tissues, and cells. In the case of osteoarthritis (OA), the degradation of cartilage is a result of both mechanical stress and biochemical factors. Natural products have already been evaluated for their potential role in the prevention and treatment of OA, providing a safe and effective adjunctive therapeutic approach. This review aimed to assess the therapeutic potential of natural products and their derivatives in osteoarthritis via a systematic search of literature after 2008, including in vitro, in vivo, ex vivo, and animal models, along with clinical trials and meta-analysis. Overall, 170 papers were obtained and screened. Here, we presented findings referring to the preventative and therapeutic potential of 17 natural products and 14 naturally occurring compounds, underlining, when available, the mechanisms implicated. The nature of OA calls to initially focus on the management of symptoms, and, in that context, several naturally occurring compounds have been utilized. Underlying a global need for more sustainable natural sources for treatment, the evidence supporting their chondroprotective potential is still building up. However, arriving at that kind of solution requires more clinical research, targeting the implications of long-term treatment, adverse effects, and epigenetic implications.

Experimental quantification of pollen with DNA metabarcoding using ITS1 and trnL

Although the use of metabarcoding to identify taxa in DNA mixtures is widely approved, its reliability in quantifying taxon abundance is still the subject of debate. In this study we investigated the relationships between the amount of pollen grains in mock solutions and the abundance of high-throughput sequence reads and how the relationship was affected by the pollen counting methodology, the number of PCR cycles, the type of markers and plant species whose pollen grains have different characteristics. We found a significant positive relationship between the number of DNA sequences and the number of pollen grains in the mock solutions. However, better relationships were obtained with light microscopy as a pollen grain counting method compared with flow cytometry, with the chloroplastic trnL marker compared with ribosomal ITS1 and with 30 when compared with 25 or 35 PCR cycles. We provide a list of recommendations to improve pollen quantification.

Current achievements and future prospects in the genetic breeding of chrysanthemum: a review

Chrysanthemum (Chrysanthemum morifolium Ramat.) is a leading flower with applied value worldwide. Developing new chrysanthemum cultivars with novel characteristics such as new flower colors and shapes, plant architectures, flowering times, postharvest quality, and biotic and abiotic stress tolerance in a time- and cost-efficient manner is the ultimate goal for breeders. Various breeding strategies have been employed to improve the aforementioned traits, ranging from conventional techniques, including crossbreeding and mutation breeding, to a series of molecular breeding methods, including transgenic technology, genome editing, and marker-assisted selection (MAS). In addition, the recent extensive advances in high-throughput technologies, especially genomics, transcriptomics, proteomics, metabolomics, and microbiomics, which are collectively referred to as omics platforms, have led to the collection of substantial amounts of data. Integration of these omics data with phenotypic information will enable the identification of genes/pathways responsible for important traits. Several attempts have been made to use emerging molecular and omics methods with the aim of accelerating the breeding of chrysanthemum. However, applying the findings of such studies to practical chrysanthemum breeding remains a considerable challenge, primarily due to the high heterozygosity and polyploidy of the species. This review summarizes the recent achievements in conventional and modern molecular breeding methods and emerging omics technologies and discusses their future applications for improving the agronomic and horticultural characteristics of chrysanthemum.

Chloroplast genome sequences of Artemisia maritima and Artemisia absinthium: Comparative analyses, mutational hotspots in genus Artemisia and phylogeny in family Asteraceae

Artemisia L. is a complex genus of medicinal importance. Publicly available chloroplast genomes of few Artemisia species are insufficient to resolve taxonomic discrepancies at species level. We report chloroplast genome sequences of two further Artemisia species: A. maritima (151,061 bp) and A. absinthium (151,193 bp). Both genomes possess typical quadripartite structure comprising of a large single copy, a small single copy and a pair of long inverted repeats. The two genomes exhibited high similarities in genome sizes, gene synteny, GC content, synonymous and non-synonymous substitutions, codon usage, amino acids frequencies, RNA editing sites, microsatellites, and oligonucleotide repeats. Transition to transversion ratio was <1. Maximum likelihood tree showed Artemisia a monophyletic genus, sister to genus Chrysanthemum. We also identified 20 highly polymorphic regions including rpoC2-rps2, trnR-UCU-trnG-UCC, rps18-rpl20, and trnL-UAG-rpl32 that could be used to develop authentic and cost-effective markers to resolve taxonomic discrepancies and infer phylogenetic relationships among Artemisia species.

Comparative Analysis of Phytochemical Composition of Gamma-Irradiated Mutant Cultivars of Chrysanthemum morifolium

The flowers of chrysanthemum species are used as a herbal tea and in traditional medicine. In addition, members of the genus have been selected to develop horticultural cultivars of diverse floral colors and capitulum forms. In this research, we investigated the phytochemical composition of eight gamma-irradiation mutant cultivars of Chrysanthemum morifolium and their original cultivars. The mutant chrysanthemum cultivars were generated by treatment with various doses of ⁶⁰Co gamma irradiation of stem cuttings of three commercial chrysanthemum cultivars as follows: ‘ARTI-Dark Chocolate’ (50Gy), ‘ARTI-Purple Lady’ (30 Gy), and ‘ARTI-Yellow Star’ (50 Gy) derived from ‘Noble Wine’; ‘ARTI-Red Star’ (50 Gy) and ‘ARTI-Rising Sun’ (30 Gy) from ‘Pinky’; ‘ARTI-Purple’ (40 Gy) and ‘ARTI-Queen’ (30 Gy) from ‘Argus’; and ‘ARTI-Rollypop’ (70 Gy) from ‘Plaisir d’amour’. Quantitative analysis of flavonoids, phenolic acids, anthocyanins, and carotenoids in the flowers of the 12 chrysanthemum cultivars was performed using high performance liquid chromatography-diode array detector-electrospray ionization mass spectrometry (HPLC-DAD-ESIMS). Essential oils from the flowers of these cultivars were analyzed by gas chromatography–mass spectrometry (GC-MS). The mutant cultivars, ‘ARTI-Dark Chocolate’, ‘ARTI-Purple Lady’, ‘ARTI-Purple’, and ‘ARTI-Queen’ showed higher total amounts of flavonoid and phenolic acid compared with those of the respective original cultivars. The mutant cultivars, ‘ARTI-Dark Chocolate’, ‘ARTI-Purple Lady’ and ‘ARTI-Purple’, which produce purple to pink petals, contained more than two-times higher amounts of anthocyanins compared with those of their original cultivars. Of the mutant cultivars, ‘ARTI-Yellow Star’ in which petal color was changed to yellow, showed the greatest accumulation of carotenoids. Ninety-nine volatile compounds were detected, of which hydrocarbons and terpenoids were abundant in all cultivars analyzed. This is the first report that demonstrated the phytochemical analysis of novel chrysanthemum cultivars derived from C. morifolium hydrid using HPLC-DAD-ESIMS and GC-MS. These findings suggest that the selected mutant chrysanthemum cultivars show potential as a functional source of phytochemicals associated with the abundance of health-beneficial components, as well as good source for horticulture and pigment industries.

Nunataks or massif de refuge? A phylogeographic study of Rhodiola crenulata (Crassulaceae) on the world's highest sky islands

Background

Quaternary climatic oscillations had tremendous effects on the current distribution of species. Here, we aim to elucidate the glacial history of Rhodiola crenulata, a perennial herb almost exclusively restricted to rock crevices on mountain peaks, and to test whether the nunatak or massif de refuge hypotheses could explain its distribution pattern.

Results

Six haplotypes and six ribotypes were detected in the cpDNA data set and the ITS data set, respectively. The divergence of R. crenulata and its closest relatives was dated have occurred ca. 0.65 Mya, during the Naynayxungla glaciation on the QTP. Mismatch distribution analysis suggested that the species experienced a range expansion around 0.31 Mya. Populations with high genetic and haplotype diversity were found on the QTP platform as well in the Hengduan Mountains. The ecological niche modeling results showed that there were suitable habitats on both the QTP platform and in the Hengduan Mountains during the LGM.

Conclusion

Our results support a scenario that both nunataks and the massif de refuge hypotheses could explain the distribution of R. crenulata. We also confirmed that Quaternary climatic oscillations could promote plant speciation in some circumstances. This study adds to a growing body of evidence suggesting that the QTP plant lineages exhibited diverse reactions to the Quaternary climatic oscillations.

Electronic supplementary material

The online version of this article (10.1186/s12862-018-1270-6) contains supplementary material, which is available to authorized users.

The complete plastid genome sequence of Chrysanthemum lucidum (Asteraceae): an endemic species of Ulleung Island of Korea

The characteristic of complete chloroplast (cp) genome sequence of Chrysanthemum lucidum, one of famous insular plant and an endemic to Ulleung Island of Korea, was firstly introduced in the present study. It was 150,985 bp and contained a large single copy region (82,786 bp) and a small single copy region (18,281 bp) which were separated by two inverted repeat regions (24,959 bp). In total, 131 genes were identified and they were consisted of 76 coding genes, eight rRNA genes, and 36 tRNA genes. Comparing to the previously reported Chrysanthemum indicum and C. x morifolium cp genomes, we found complete inversion of SSC region in this taxa. rpoC1 gene was pseudogenes due to 1 bp insertion of poly-A sequence in the 3' of exon 2.

Climate Is Not All: Evidence From Phylogeography of Rhodiola fastigiata (Crassulaceae) and Comparison to Its Closest Relatives

How geological events and climate oscillations in the Pleistocene glaciation shaped the geographic distribution of genetic variation of species on the Qinghai-Tibetan Plateau (QTP) and its adjacent areas has been extensively studied. However, little studies have investigated whether closely related species in the same genus with similar physiological and life history traits responded similarly to the glacial climatic oscillations. If this is not the case, we would expect that the population histories of studied species were not driven by extrinsic environmental changes alone. Here we conducted a phylogeographic study of a succulent alpine plant Rhodiola fastigiata, using sequences from chloroplast genome and nrITS region, as well as ecological niche modeling. The results of R. fastigiata were compared to other congeneric species that have been studied, especially to R. alsia and R. crenulata. We found that for both markers, two geographic groups could be revealed, corresponding to the QTP plateau and the Hengduan Mountains, respectively, indicating isolated refugia in those two areas. The two groups diverged 1.23 Mya during the Pleistocene. We detected no significant population expansion by mismatch distribution analysis and Bayesian Skyline Plot. We found that even these similar species with similar physiological and life history traits have had different demographic histories in the Quaternary glacial periods. Our comparative phylogeographic study sheds new lights into phylogeographic research that extrinsic environmental changes are not the only factor that can drive population demography, and other factors, such as coevolved interactions between plants and their specialized pathogens, that probably played a role need to be examined with more case studies.

Comparative transcriptome analysis reveals whole-genome duplications and gene selection patterns in cultivated and wild Chrysanthemum species

Comparative transcriptome analysis of wild and cultivated chrysanthemums provides valuable genomic resources and helps uncover common and divergent patterns of genome and gene evolution in these species. Plants are unique in that they employ polyploidy (or whole-genome duplication, WGD) as a key process for speciation and evolution. The Chrysanthemum genus is closely associated with hybridization and polyploidization, with Chrysanthemum species exhibiting diverse ploidy levels. The commercially important species, C. morifolium is an allohexaploid plant that is thought to have originated via the hybridization of several Chrysanthemum species, but the genomic and molecular evolutionary mechanisms remain poorly understood. In the present study, we sequenced and compared the transcriptomes of C. morifolium and the wild Korean diploid species, C. boreale. De novo transcriptome assembly revealed 11,318 genes in C. morifolium and 10,961 genes in C. boreale, whose functions were annotated by homology searches. An analysis of synonymous substitution rates (Ks) of paralogous and orthologous genes suggested that the two Chrysanthemum species commonly experienced the Asteraceae paleopolyploidization and recent genome duplication or triplication before the divergence of these species. Intriguingly, C. boreale probably underwent rapid diploidization, with a reduction in chromosome number, whereas C. morifolium maintained the original chromosome number. Analysis of the ratios of non-synonymous to synonymous nucleotide substitutions (Ka/Ks) between orthologous gene pairs indicated that 107 genes experienced positive selection, which may have been crucial for the adaptation, domestication, and speciation of Chrysanthemum.

A SNP-Enabled Assessment of Genetic Diversity, Evolutionary Relationships and the Identification of Candidate Genes in Chrysanthemum

Varieties of the economically important ornamental species chrysanthemum have been bred to fit a number of market niches, but the genetic basis and evolutionary relationships among various cultivated types are poorly understood. Here, a DNA marker-based analysis of 199 chrysanthemum entries representing each of the five cultivated types is presented. A set of >90,000 single nucleotide polymorphisms (SNPs) associated with a minor allele frequency of at least 5% was defined, and used to perform a phylogenetic analysis which corresponded well with the phenotypic classification. The analysis revealed that the small-flowered types, spray cut chrysanthemum (SCC) and potted and ground chrysanthemum (PGC), are more closely related to the wild progenitor species (WC) than are the large-flowered ones, disbud cut chrysanthemum (DCC) and traditional chrysanthemum (TC); and the PGC type was closest. Some 550 genetic regions appeared to have experienced selection in the separation of potted and ground-cover types from disbud cut types, and that between potted and ground-cover types from traditional types. A genome-wide association analysis revealed that seven SNPs lying within six genes were predictive of three important traits (ray floret type, cultivated type and flower shape), but no association with flower color was detected. The study has provided a number of novel insights into evolutionary relationships, the population structure and the genetic basis of some key ornamental traits.

Complete chloroplast genomes from apomictic Taraxacum (Asteraceae): Identity and variation between three microspecies

Chloroplast DNA sequences show substantial variation between higher plant species, and less variation within species, so are typically excellent markers to investigate evolutionary, population and genetic relationships and phylogenies. We sequenced the plastomes of Taraxacum obtusifrons Markl. (O978); T. stridulum Trávniček ined. (S3); and T. amplum Markl. (A978), three apomictic triploid (2n = 3x = 24) dandelions from the T. officinale agg. We aimed to characterize the variation in plastomes, define relationships and correlations with the apomictic microspecies status, and refine placement of the microspecies in the evolutionary or phylogenetic context of the Asteraceae. The chloroplast genomes of accessions O978 and S3 were identical and 151,322 bp long (where the nuclear genes are known to show variation), while A978 was 151,349 bp long. All three genomes contained 135 unique genes, with an additional copy of the trnF-GGA gene in the LSC region and 20 duplicated genes in the IR region, along with short repeats, the typical major Inverted Repeats (IR1 and IR2, 24,431bp long), and Large and Small Single Copy regions (LSC 83,889bp and SSC 18,571bp in O978). Between the two Taraxacum plastomes types, we identified 28 SNPs. The distribution of polymorphisms suggests some parts of the Taraxacum plastome are evolving at a slower rate. There was a hemi-nested inversion in the LSC region that is common to Asteraceae, and an SSC inversion from ndhF to rps15 found only in some Asteraceae lineages. A comparative repeat analysis showed variation between Taraxacum and the phylogenetically close genus Lactuca, with many more direct repeats of 40bp or more in Lactuca (1% larger plastome than Taraxacum). When individual genes and non-coding regions were for Asteraceae phylogeny reconstruction, not all showed the same evolutionary scenario suggesting care is needed for interpretation of relationships if a limited number of markers are used. Studying genotypic diversity in plastomes is important to characterize the nature of evolutionary processes in nuclear and cytoplasmic genomes with the different selection pressures, population structures and breeding systems.

Towards development of new ornamental plants: status and progress in wide hybridization

The present review provides insights into the key findings of the hybridization process, crucial factors affecting the adaptation of new technologies within wide hybridization of ornamental plants and presents perspectives of further development of this strategy. Wide hybridization is one of the oldest breeding techniques that contributed enormously to the development of modern plant cultivars. Within ornamental breeding, it represents the main source of genetic variation. During the long history of wide hybridization, a number of methods were implemented allowing the evolution from a conventional breeding tool into a modern methodology. Nowadays, the research on model plants and crop species increases our understanding of reproductive isolation among distant species and partly explains the background of the traditional approaches previously used for overcoming hybridization barriers. Characterization of parental plants and hybrids is performed using molecular and cytological techniques that strongly facilitate breeding processes. Molecular markers and sequencing technologies are used for the assessment of genetic relationships among plants, as the genetic distance is typically depicted as one of the most important factors influencing cross-compatibility in hybridization processes. Furthermore, molecular marker systems are frequently applied for verification of hybrid state of the progeny. The flow cytometry and genomic in situ hybridization are used in the assessment of hybridization partners and characterization of hybrid progeny in relation to genome stabilization as well as genome recombination and introgression. In the future, new research and technologies are likely to provide more detailed information about genes and pathways responsible for interspecific reproductive isolation. Ultimately, this knowledge will enable development of strategies for obtaining compatible lines for hybrid production. Recent development in sequencing technologies and availability of sequence data will also facilitate creation of new molecular markers that will advance marker-assisted selection in hybridization process.

The polyploidy and its key role in plant breeding

This article provides an up-to-date review concerning from basic issues of polyploidy to aspects regarding the relevance and role of both natural and artificial polyploids in plant breeding programs. Polyploidy is a major force in the evolution of both wild and cultivated plants. Polyploid organisms often exhibit increased vigor and, in some cases, outperform their diploid relatives in several aspects. This remarkable superiority of polyploids has been the target of many plant breeders in the last century, who have induced polyploidy and/or used natural polyploids in many ways to obtain increasingly improved plant cultivars. Some of the most important consequences of polyploidy for plant breeding are the increment in plant organs ("gigas" effect), buffering of deleterious mutations, increased heterozygosity, and heterosis (hybrid vigor). Regarding such features as tools, cultivars have been generated with higher yield levels, improving the product quality and increasing the tolerance to both biotic and abiotic stresses. In some cases, when the crossing between two species is not possible because of differences in ploidy level, polyploids can be used as a bridge for gene transferring between them. In addition, polyploidy often results in reduced fertility due to meiotic errors, allowing the production of seedless varieties. On the other hand, the genome doubling in a newly formed sterile hybrid allows the restoration of its fertility. Based on these aspects, the present review initially concerns the origin, frequency and classification of the polyploids, progressing to show the revolution promoted by the discovery of natural polyploids and polyploidization induction in the breeding program status of distinct crops.

Identification and Characterization of CYC-Like Genes in Regulation of Ray Floret Development in Chrysanthemum morifolium

Chrysanthemum morifolium, one of the most economically important ornamental crops worldwide, is well-known for the elaborate and complex inflorescence which is composed of both bilaterally symmetrical ray florets and radially symmetrical disc florets. Despite continuing efforts, the molecular mechanisms underlying regulation of the two flower types are still unclear so far. CYC-like proteins have been shown to control flower symmetry or regulate flower-type identity in several angiosperm plant lineages. In this study, we conducted comparative analysis of the CmCYC2 genes in two chrysanthemum cultivars and their F1 progenies with various whorls of ray florets. Six CmCYC genes were identified and sequenced, all of which were grouped into the CYC2 subclade. All the six CmCYC2 genes were predominantly expressed in reproductive organs, and in particular in the petal of ray florets. Of these genes, the transcription level of CmCYC2c was highly up-regulated in ray florets of the double-ray flowered heads. In addition, the result that CmCYC2c was highly expressed at key developing stages indicates its role in regulating petal development. Furthermore, overexpression of CmCYC2c in C. lavandulifolium, one of the original species of C. morifolium, led to significant increase in flower numbers and petal ligule length of ray florets. Besides CmCYC2c, the expression of CmCYC2f was also significantly up-regulated in transgenic lines, implying a possible role in regulating development of ray florets. Both results of expression patterns and transgenic phenotypes suggest that CmCYC2c is involved in regulating ray floret identity in the chrysanthemum. This study will be useful for genetic manipulation of flower shape in chrysanthemum and hence promote the process of molecular breeding.

A genome-scale mining strategy for recovering novel rapidly-evolving nuclear single-copy genes for addressing shallow-scale phylogenetics in Hydrangea

Background

Identifying orthologous molecular markers that potentially resolve relationships at and below species level has been a major challenge in molecular phylogenetics over the past decade. Non-coding regions of nuclear low- or single-copy markers are a vast and promising source of data providing information for shallow-scale phylogenetics. Taking advantage of public transcriptome data from the One Thousand Plant Project (1KP), we developed a genome-scale mining strategy for recovering potentially orthologous single-copy markers to address low-scale phylogenetics. Our marker design targeted the amplification of intron-rich nuclear single-copy regions from genomic DNA. As a case study we used Hydrangea section Cornidia, one of the most recently diverged lineages within Hydrangeaceae (Cornales), for comparing the performance of three of these nuclear markers to other “fast” evolving plastid markers.

Results

Our data mining and filtering process retrieved 73 putative nuclear single-copy genes which are potentially useful for resolving phylogenetic relationships at a range of divergence depths within Cornales. The three assessed nuclear markers showed considerably more phylogenetic signal for shallow evolutionary depths than conventional plastid markers. Phylogenetic signal in plastid markers increased less markedly towards deeper evolutionary divergences. Potential phylogenetic noise introduced by nuclear markers was lower than their respective phylogenetic signal across all evolutionary depths. In contrast, plastid markers showed higher probabilities for introducing phylogenetic noise than signal at the deepest evolutionary divergences within the tribe Hydrangeeae (Hydrangeaceae).

Conclusions

While nuclear single-copy markers are highly informative for shallow evolutionary depths without introducing phylogenetic noise, plastid markers might be more appropriate for resolving deeper-level divergences such as the backbone relationships of the Hydrangeaceae family and deeper, at which non-coding parts of nuclear markers could potentially introduce noise due to elevated rates of evolution. The herein developed and demonstrated transcriptome based mining strategy has a great potential for the design of novel and highly informative nuclear markers for a range of plant groups and evolutionary scales.

Electronic supplementary material

The online version of this article (doi:10.1186/s12862-015-0416-z) contains supplementary material, which is available to authorized users.

Comparative analysis of chrysanthemum transcriptome in response to three RNA viruses: Cucumber mosaic virus, Tomato spotted wilt virus and Potato virus X

The chrysanthemum is one of popular flowers in the world and a host for several viruses. So far, molecular interaction studies between the chrysanthemum and viruses are limited. In this study, we carried out a transcriptome analysis of chrysanthemum in response to three different viruses including Cucumber mosaic virus (CMV), Tomato spotted wilt virus (TSWV) and Potato virus X (PVX). A chrysanthemum 135K microarray derived from expressed sequence tags was successfully applied for the expression profiles of the chrysanthemum at early stage of virus infection. Finally, we identified a total of 125, 70 and 124 differentially expressed genes (DEGs) for CMV, TSWV and PVX, respectively. Many DEGs were virus specific; however, 33 DEGs were commonly regulated by three viruses. Gene ontology (GO) enrichment analysis identified a total of 132 GO terms, and of them, six GO terms related stress response and MCM complex were commonly identified for three viruses. Several genes functioning in stress response such as chitin response and ethylene mediated signaling pathway were up-regulated indicating their involvement in establishment of host immune system. In particular, TSWV infection significantly down-regulated genes related to DNA metabolic process including DNA replication, chromatin organization, histone modification and cytokinesis, and they are mostly targeted to nucleosome and MCM complex. Taken together, our comparative transcriptome analysis revealed several genes related to hormone mediated viral stress response and DNA modification. The identified chrysanthemums genes could be good candidates for further functional study associated with resistant to various plant viruses.