<i>De novo</i>whole-genome assembly of<i>Chrysanthemum makinoi</i>, a key wild chrysanthemum

Lieshout, Natascha van; Kaauwen, Martijn van; Kodde, Linda; Arens, Paul; Smulders, M.J.M.; Visser, R.G.F.; Finkers, Richard

doi:10.1093/g3journal/jkab358

Cited by 15 publications

(10 citation statements)

References 71 publications

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“…The combination of cp genome and high-throughput sequencing technology has become an effective means of plant genetic resources research, which facilitates the study of Chrysanthemum classification and genetic resources ( Tyagi et al, 2020 ; Masuda et al, 2022 ). The accumulation of whole genome sequencing data of Chrysanthemum ( Song et al, 2018 ; Nakano et al, 2021 ; van Lieshout et al, 2022 ) and relevant taxonomic groups will enable the comprehensive phylogenomic analyses to reveal the hybridization/polyploidization events leading to the speciation and formation of CM. The assembly and annotation of more high-quality Chrysanthemum genomes will help to elucidate the genus evolution and its contributions to gene abundance/function.…”

Section: Conclusion and Prospectsmentioning

confidence: 99%

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

et al. 2022

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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.

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Section: Conclusion and Prospectsmentioning

confidence: 99%

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

et al. 2022

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“…they were ultrafragmented. Such fragmentation was similarly observed in the de novo assemblies of diploid Chrysanthemum species genomes obtained at an early stage [ 20 , 44 ] because repetitive sequences occupied >68.6% of the whole genome in the genus Chrysanthemum [ 20 , 29 , 44 , 49 ]. In this study, the high ratio of repetitive sequences could be a major cause of the failure in assembling longer sequences in cultivated chrysanthemums.…”

Section: Discussionmentioning

confidence: 77%

A genome-wide association and fine-mapping study of white rust resistance in hexaploid chrysanthemum cultivars with a wild diploid reference genome

Sumitomo

Shirasawa

Isobe

et al. 2022

Horticulture Research

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White rust caused by Puccinia horiana is one of the most serious diseases of chrysanthemum (Chrysanthemum × morifolium). In this study, we report the DNA markers associated with resistance against P. horiana via a simple approach using the genome of a wild diploid relative, Chrysanthemum seticuspe. First, we identified the important region of the genome in the resistant cultivar “Ariesu” via a genome-wide association study. Simplex single nucleotide polymorphism (SNP) markers mined from ddRAD-Seq were used in a biparental population originating from crosses between resistant “Ariesu” and susceptible “Yellow Queen”. The C. seticuspe genome was used as a reference. For the fine mapping of P. horiana resistance locus 2 (Phr2), a comparative whole genome sequencing study was conducted. Although the genome sequences of chrysanthemum cultivars assembled via the short-read approach were fragmented, reliable genome alignments were reconstructed by mapping onto the chromosome level of the C. seticuspe pseudomolecule. Base variants were then identified by comparing the assembled genome sequences of resistant “Ariesu” and susceptible “Yellow Queen”. Consequently, SNP markers that were closer to Phr2 compared with ddRAD-Seq markers were obtained. These SNP markers co-segregated with resistance in F1 progenies originating from resistant “Ariesu” and showed robust transferability for detecting Phr2-conferring resistance among chrysanthemum genetic resources. The wild C. seticuspe pseudomolecule, a de facto monoploid genome used for ddRAD-Seq analysis and assembled genome sequence comparison, demonstrated this method’s utility as a model for developing DNA markers in hexaploid chrysanthemum cultivars.

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“…Recently, with the release of the Asteraceae genome information ( Badouin et al., 2017 ; Reyes-Chin-Wo et al., 2017 ; Song et al, 2018 ; Liu et al., 2020 ; Nakano et al., 2021 ; van Lieshout et al., 2022 ; Wen et al., 2022 ), the identification of gene families based on a genome-wide level has become feasible. Here, C .…”

Section: Introductionmentioning

confidence: 99%

Genome-wide identification of the MIKCc-type MADS-box gene family in Chrysanthemum lavandulifolium reveals their roles in the capitulum development

Zhang

Kong

et al. 2023

Front. Plant Sci.

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Chrysanthemum ×morifolium is well known throughout the world for its diverse and exquisite flower types. However, due to the complicated genetic background of C. ×morifolium, it is difficult to understand the molecular mechanism of its flower development. And it limits the molecular breeding of improving chrysanthemum flower types. C. ×morifolium has the typical radial capitulum, and many researches showed that the members of the MIKCc-type MADS box gene family play a key role in the formation and development of the capitulum. However, it has been difficult to isolate the important MIKCc and investigate their roles in this process due to the lack of genomic information in chrysanthemum. Here, we identified MIKCc-type MADS box genes at whole genome-wide level in C. lavandulifolium, a diploid species closely related to C. ×morifolium, and investigated their roles in capitulum development by gene expression pattern analysis and protein interaction analysis. A total of 40 ClMIKCc were identified and were phylogenetically grouped into 12 clades. Members of all clades showed different enriched expression patterns during capitulum formation. We speculate that the E-class genes in C. lavandulifolium underwent subfunctionalization because they have a significantly expanded, more diverse expression patterns, and specifically tissue expression than AtSEPs. Meanwhile, we detected the C-class expressed in disc floret corolla, which could be the clue to explore the morphological differences between disc and ray floret corolla. In addition, the potential roles of some MIKCcs in complex inflorescence formation were explored by comparing the number and phylogenetic relationship of MIKCc subfamily members in Asteraceae with different capitulum types. Members of the FLC branch in Asteraceae were found to be possibly related to the differentiation and development of the ray floret.

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De novowhole-genome assembly ofChrysanthemum makinoi, a key wild chrysanthemum

Cited by 15 publications

References 71 publications

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

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

A genome-wide association and fine-mapping study of white rust resistance in hexaploid chrysanthemum cultivars with a wild diploid reference genome

Genome-wide identification of the MIKCc-type MADS-box gene family in Chrysanthemum lavandulifolium reveals their roles in the capitulum development

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