Pangenome and resequencing analyses reveal flowering evolution and genetic control in Cerasus

Prunus subgenus Cerasus contains numerous species with ornamental, edible, and medicinal value. However, limited genomic resources have constrained systematic analyses of structural variation and the genetic basis of key phenological traits in this group. Here, we assemble eight genomes from diverse Cerasus species. Together with 13 published genomes, we construct a pangenome of 21 accessions representing 17 species. Phenological observations reveal substantial variation in flowering time. Integrating comparative genomics, transcriptomics, and population genetic analyses highlight candidate regulators of flowering time. We find that AGAMOUS-LIKE 9 (AGL9) is strongly associated with flowering progression. Both ectopic expression and transient overexpression of PavAGL9 can accelerate post-dormancy flowering progression. We reveal that PavBPC6 binds the PavAGL9 promoter and represses its transcription, indicating a negative regulatory role. Furthermore, PavAGL9 interacts physically with PavSEP1 and PavPMADS2, suggesting synergistic roles in floral organ development. Our pangenome resource establishes a comprehensive genomic framework for Cerasus and provides insights into the regulation of flowering progression. Prunus subgenus Cerasus comprises over 70 species with ornamental, edible, and medicinal value. Here, the authors assemble eight genomes from wild and cultivated Cerasus species, construct pangenome together with 13 public genomes, and uncover the evolutionary origin and genetic determinants of flower development.

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Publication Details

Journal
Nature Communications
Published
2026-05-27
DOI
https://doi.org/10.1038/s41467-026-72832-8
Primary Topic
Plant Molecular Biology Research
Type
article
Field-Weighted Citation Impact
0.00

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article

Pangenome and resequencing analyses reveal flowering evolution and genetic control in Cerasus

C L Zhang, Mitsuho Nakagomi, Qi Zhao, Xiaojuan An et al.
Nature Communications
Plant Molecular Biology Research
article

Pangenome and resequencing analyses reveal flowering evolution and genetic control in Cerasus

C L Zhang, Mitsuho Nakagomi, Qi Zhao, Xiaojuan An, D.A.A. ELISABETH, Zhengxin Lv, Ruie Liu, Hongzhang Xue, Yahui Lei, B Liu, Yan Zhang, Hui Li, Congli Liu, Yi Xu, Shengchang Duan, Yaqin Wu, Fei Yu, Anthony Bernard, Xunju Liu, Chunjin Yin, Zongyi Sun, Lixia Yu, Long Chen, Xi Zhang, Jijun Zhu, Lei Peng, Fangdong Li, Yi-Xiang Wang, Linlin Fang, Ming Li, Yuliang Cai, Lu Han, Wei Zheng, Lei Wang, Dawei Li, Songtao Jiu, Shiping Wang, Taoxian Zhang, Yang Dong, Xiao Dong, Zhuo Zhang, Wenbo Chen, Li Wang, Yue Huang
article en

Abstract

Prunus subgenus Cerasus contains numerous species with ornamental, edible, and medicinal value. However, limited genomic resources have constrained systematic analyses of structural variation and the genetic basis of key phenological traits in this group. Here, we assemble eight genomes from diverse Cerasus species. Together with 13 published genomes, we construct a pangenome of 21 accessions representing 17 species. Phenological observations reveal substantial variation in flowering time. Integrating comparative genomics, transcriptomics, and population genetic analyses highlight candidate regulators of flowering time. We find that AGAMOUS-LIKE 9 (AGL9) is strongly associated with flowering progression. Both ectopic expression and transient overexpression of PavAGL9 can accelerate post-dormancy flowering progression. We reveal that PavBPC6 binds the PavAGL9 promoter and represses its transcription, indicating a negative regulatory role. Furthermore, PavAGL9 interacts physically with PavSEP1 and PavPMADS2, suggesting synergistic roles in floral organ development. Our pangenome resource establishes a comprehensive genomic framework for Cerasus and provides insights into the regulation of flowering progression. Prunus subgenus Cerasus comprises over 70 species with ornamental, edible, and medicinal value. Here, the authors assemble eight genomes from wild and cultivated Cerasus species, construct pangenome together with 13 public genomes, and uncover the evolutionary origin and genetic determinants of flower development.

Nature CommunicationsVol. 17(1)
Anhui Agricultural University (CN), Université de Bordeaux (FR), Dalian Institute of Chemical Physics (CN), Shanghai Jiao Tong University (CN), Yunnan Agricultural University (CN), Shanghai Botanical Garden (CN), Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement (FR), Biologie du Fruit et Pathologie (FR), Yantai Academy of Agricultural Sciences (CN), Yunnan Academy of Agricultural Sciences (CN), State Forestry and Grassland Administration (CN), Shanghai Chenshan Plant Science Research Center (CN), Institute of Pomology (CN), Zhengzhou Fruit Research Institute (CN), Beijing Academy of Agricultural and Forestry Sciences (CN), Enshi Tujia and Miao Autonomous Prefecture Academy of Agricultural Sciences (CN), Grandomics (China) (CN), Hebei Academy of Agriculture and Forestry Sciences (CN), Sichuan Academy of Agricultural Sciences (CN), Tianshui Normal University (CN), Gifu University (JP), Zhejiang University (CN), Northwest A&F University (CN)
Natural Science Foundation of Shanghai, National Natural Science Foundation of China, Shanghai Jiao Tong University, Northeast Agricultural University, Xinjiang Agricultural University, Earmarked Fund for China Agriculture Research System, Key Research and Development Projects of Shaanxi Province
Openalex Percentile: Top 7%
Plant Molecular Biology Research
DOIOpen Access PDFOpenAlex
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