ArticleDNA research : an international journal for rapid publication of reports on genes and genomes2019
De novo whole-genome assembly in Chrysanthemum seticuspe, a model species of Chrysanthemums, and its application to genetic and gene discovery analysis.
Article in DNA research : an international journal for rapid publication of reports on genes and genomes, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 50 papers.
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50 citing papers in PubMed.
- The origin and domestication of modern cultivated Chrysanthemum × morifolium.Nature plants · 2026Article
- CmDREBa regulates the perennial growth habit of chrysanthemum in response to prolonged chilling.Nature communications · 2026Article
- Chromosome-level genome assembly of the Gerbera (Gerbera hybrida) using HiFi long-read and Hi-C technologies.DNA research : an international journal for rapid publication of reports on genes and genomes · 2026Article
- QTL detection and candidate gene identification for prostrate growth habit in interspecific crosses of wild chrysanthemum (Horticulture research · 2025Article
- Advancing ornamental plant breeding through genomic technologies: opportunities, challenges, and future directions.Functional & integrative genomics · 2025Review
- Assessing Functional Conservation AmongstPlants (Basel, Switzerland) · 2025Article
- Designing of future ornamental crops: a biotechnological driven perspective.Horticulture research · 2023Article
- Detection of Transcription Factors Related to Axillary Bud Development after Exposure to Cold Conditions in HexaploidPlants (Basel, Switzerland) · 2023Article
- Overcoming Difficulties in Molecular Biological Analysis through a Combination of Genetic Engineering, Genome Editing, and Genome Analysis in HexaploidPlants (Basel, Switzerland) · 2023Review
- Two-step model of paleohexaploidy, ancestral genome reshuffling and plasticity of heat shock response in Asteraceae.Horticulture research · 2023Article
- Phylogenomics and morphological evolution of the mega-diverse genus Artemisia (Asteraceae: Anthemideae): implications for its circumscription and infrageneric taxonomy.Annals of botany · 2023Article
- Analyses of a chromosome-scale genome assembly reveal the origin and evolution of cultivated chrysanthemum.Nature communications · 2023Article
- Discovering the Repeatome of Five Species Belonging to the Asteraceae Family: A Computational Study.Plants (Basel, Switzerland) · 2023Article
- Transcriptome-based variations effectively untangling the intraspecific relationships and selection signals in Xinyang Maojian tea population.Frontiers in plant science · 2023Article
- Current insights and advances into plant male sterility: new precision breeding technology based on genome editing applications.Frontiers in plant science · 2023Review
- Creating novel ornamentalsFrontiers in plant science · 2023Review
- The Current Developments in Medicinal Plant Genomics Enabled the Diversification of Secondary Metabolites' Biosynthesis.International journal of molecular sciences · 2022Review
- Whole-transcriptome profiles of Chrysanthemum seticuspe improve genome annotation and shed new light on mRNA-miRNA-lncRNA networks in ray florets and disc florets.BMC plant biology · 2022Article
- Towards the Improvement of Ornamental Attributes in Chrysanthemum: Recent Progress in Biotechnological Advances.International journal of molecular sciences · 2022Review
- Development of a Transformation System and Locus Identification Pipeline for T-DNA inInternational journal of molecular sciences · 2022Article
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14 authors.
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Abstract
Cultivated chrysanthemum (Chrysanthemum morifolium Ramat.) is one of the most economically important ornamental crops grown worldwide. It has a complex hexaploid genome (2n = 6x = 54) and large genome size. The diploid Chrysanthemum seticuspe is often used as a model of cultivated chrysanthemum, since the two species are closely related. To expand our knowledge of the cultivated chrysanthemum, we here performed de novo whole-genome assembly in C. seticuspe using the Illumina sequencing platform. XMRS10, a C. seticuspe accession developed by five generations of self-crossing from a self-compatible strain, AEV2, was used for genome sequencing. The 2.72 Gb of assembled sequences (CSE_r1.0), consisting of 354,212 scaffolds, covered 89.0% of the 3.06 Gb C. seticuspe genome estimated by k-mer analysis. The N50 length of scaffolds was 44,741 bp. For protein-encoding genes, 71,057 annotated genes were deduced (CSE_r1.1_cds). Next, based on the assembled genome sequences, we performed linkage map construction, gene discovery and comparative analyses for C. seticuspe and cultivated chrysanthemum. The generated C. seticuspe linkage map revealed skewed regions in segregation on the AEV2 genome. In gene discovery analysis, candidate flowering-related genes were newly found in CSE_r1.1_cds. Moreover, single nucleotide polymorphism identification and annotation on the C. × morifolium genome showed that the C. seticuspe genome was applicable to genetic analysis in cultivated chrysanthemums. The genome sequences assembled herein are expected to contribute to future chrysanthemum studies. In addition, our approach demonstrated the usefulness of short-read genome assembly and the importance of choosing an appropriate next genome sequencing technology based on the purpose of the post-genome analysis.
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