Chromosome-scale genome assembly of Prunus pusilliflora provides novel insights into genome evolution, disease resistance, and dormancy release in Cerasus L.

Abstract

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 viniferum, Phytophthora capsici, and Pseudomonas syringae pv. tomato (Pst) DC3000 infections than cultivated Prunus avium. P. 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.

Acknowledgements

This study was funded by the Shanghai Agriculture Applied Technology Development Program, China (grant no. 2022-02-08-00-12-F01111), the China Agriculture Research System (grant no. CARS-30-2-08), the National Natural Science Foundation of China (grant no. 32102347), the Shanghai Sailing Program (grant no. 21YF1422100), and the Startup Fund for Young Faculty at SJTU (grant no. 21X010500643). We thank Dr. Xiaoyu Tu from Shanghai Jiao Tong University for proofreading the manuscript. We thank Dr. Wei Wu, Dr. Gang Yu, and Dr. Jiaqi Liu from Shanghai Jiao Tong University for their technical assistance. We thank Prof. Jiang Lu from Shanghai Jiao Tong University for providing the C. viniferum, P. capsici, P. syringae pv. tomato (Pst) DC3000, and B. cinerea samples used in this study.

Authors contributions

C.Z. and Y.D. conceived and designed the experiments; S.J. collected the samples, performed disease resistance tests, and drafted the manuscript; B.C. and X.D. conducted the assembly and annotations and contributed to the sequencing data analyses; Z.L., Y.W., and Y.X. performed the disease resistance tests; C.Y., Z.Z., and S.L. collected the samples; M.L., J.Z., and J.W. worked on the phenotyping; S.Z., X.L., M.A.M., and W.S. performed the statistical analysis. R.L., L.W., G.Y., Q.J., E.D., Y.L., L.Y., and S.W. participated in discussions and provided valuable advice. All authors provided final approval for publication.

Data availability

The raw genome sequencing data of Ppus are available at the National Genomics Data Center (https://ngdc.cncb.ac.cn/) under BioProject number PRJCA010538. All data are available from the corresponding authors upon request.

Conflict of interest

The authors declare no competing financial interest.

Supplementary data

Supplementary data is available at Horticulture Research online.

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