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Article|10 Apr 2023|OPEN
Chromosome-scale genome assembly of Prunus pusilliflora provides novel insights into genome evolution, disease resistance, and dormancy release in Cerasus L. 
Songtao Jiu1,7 , Baozheng Chen2,7 , Xiao Dong2 , Zhengxin Lv1 , Yuxuan Wang1 , Chunjin Yin3 , Yan Xu1 , Sen Zhang1 , Jijun Zhu4 , Jiyuan Wang1 , Xunju Liu1 , Wanxia Sun1 , Guoqian Yang1 , Meng Li5 , Shufeng Li3 , Zhuo Zhang1 , Ruie Liu1 , Lei Wang1 , Muhammad Aamir Manzoor1 , Quero-García José6 , Shiping Wang1 , Yahui Lei2 , Ling Yang2 and Elisabeth Dirlewanger6 , Yang Dong2 , , Caixi Zhang,1 ,
1Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, P. R. China
2College of Food Science and Technology, Yunnan Agricultural University, Kunming, Yunnan Province, 650201, P. R. China
3Dali Bai Autonomous Prefecture Academy of Agricultural Sciences and Extension, Dali, Yunnan Province, 671600, P. R. China
4Shanghai Botanical Garden, Shanghai, 200231, P. R. China
5College of Biology and the Environment, Nanjing Forestry University, Nanjing, Jiangsu Province, 200037, P. R. China
6INRAe, UMR 1332 de Biologie du Fruit et Pathologie, 33140 Villenave d’Ornon, France
7Co-first author, Equal contribution
*Corresponding author. E-mail:,

Horticulture Research 10,
Article number: uhad062 (2023)
Views: 318

Received: 10 Oct 2022
Accepted: 02 Apr 2023
Published online: 10 Apr 2023


Prunus pusilliflora is a wild cherry germplasm resource distributed mainly in Southwest China. Despite its ornamental and economic value, a high-quality assembled P. pusilliflora genome is unavailable, hindering our understanding of its genetic background, population diversity, and evolutionary processes. Here, we de novo assembled a chromosome-scale P. pusilliflora genome using Oxford Nanopore, Illumina, and chromosome conformation capture sequencing. The assembled genome size was 309.62 Mb, with 76 scaffolds anchored to eight pseudochromosomes. We predicted 33 035 protein-coding genes, functionally annotated 98.27% of them, and identified repetitive sequences covering 49.08% of the genome. We found that P. pusilliflora is closely related to Prunus serrulata and Prunus yedoensis, having diverged from them ~41.8 million years ago. A comparative genomic analysis revealed that P. pusilliflora has 643 expanded and 1128 contracted gene families. Furthermore, we found that P. pusilliflora is more resistant to Colletotrichum viniferumPhytophthora capsici, and Pseudomonas syringae pv. tomato (Pst) DC3000 infections than cultivated Prunus aviumP. pusilliflora also has considerably more nucleotide-binding site-type resistance gene analogs than P. avium, which explains its stronger disease resistance. The cytochrome P450 and WRKY families of 263 and 61 proteins were divided into 42 and 8 subfamilies respectively in P. pusilliflora. Furthermore, 81 MADS-box genes were identified in P. pusilliflora, accompanying expansions of the SVP and AGL15 subfamilies and loss of the TM3 subfamily. Our assembly of a high-quality P. pusilliflora genome will be valuable for further research on cherries and molecular breeding.