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

Aiping Song, Jiangshuo Su, Haibin Wang, Zhongren Zhang, Xingtan Zhang, Yves Peer, Fei Chen, Weimin Fang, Zhiyong Guan, Fei Zhang, Zhenxing Wang, Likai Wang, Baoqing Ding, Shuang Zhao, Lian Ding, Ye Liu, Lijie Zhou, Jun He, Diwen Jia, Jiali Zhang, Chuwen Chen, Zhongyu Yu, Daojin Sun, Jiafu Jiang (), Sumei Chen () and Fadi Chen ()
Additional contact information
Aiping Song: Nanjing Agricultural University
Jiangshuo Su: Nanjing Agricultural University
Haibin Wang: Nanjing Agricultural University
Zhongren Zhang: Novogene Bioinformatics Institute
Xingtan Zhang: Chinese Academy of Agricultural Sciences
Yves Peer: Nanjing Agricultural University
Fei Chen: Hainan University & Hainan Yazhou Bay Seed Laboratory
Weimin Fang: Nanjing Agricultural University
Zhiyong Guan: Nanjing Agricultural University
Fei Zhang: Nanjing Agricultural University
Zhenxing Wang: Nanjing Agricultural University
Likai Wang: Nanjing Agricultural University
Baoqing Ding: Nanjing Agricultural University
Shuang Zhao: Nanjing Agricultural University
Lian Ding: Nanjing Agricultural University
Ye Liu: Nanjing Agricultural University
Lijie Zhou: Nanjing Agricultural University
Jun He: Nanjing Agricultural University
Diwen Jia: Nanjing Agricultural University
Jiali Zhang: Nanjing Agricultural University
Chuwen Chen: Nanjing Agricultural University
Zhongyu Yu: Nanjing Agricultural University
Daojin Sun: Nanjing Agricultural University
Jiafu Jiang: Nanjing Agricultural University
Sumei Chen: Nanjing Agricultural University
Fadi Chen: Nanjing Agricultural University

Nature Communications, 2023, vol. 14, issue 1, 1-15

Abstract: Abstract 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.

Date: 2023
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DOI: 10.1038/s41467-023-37730-3

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