Haplotype-resolved genome assembly for tetraploid Chinese cherry (Prunus pseudocerasus) offers insights into fruit firmness

Abstract

Chinese cherry (Prunus pseudocerasus) holds considerable importance as one of the primary stone fruit crops in China. However, artificially improving its traits and genetic analysis are challenging due to lack of high-quality genomic resources, which mainly result from difficulties associated with resolving its tetraploid and highly heterozygous genome. Herein, we assembled a chromosome-level, haplotype-resolved genome of the cultivar ‘Zhuji Duanbing’, comprising 993.69 Mb assembled into 32 pseudochromosomes using PacBio HiFi, Oxford Nanopore, and Hi-C. Intra-haplotype comparative analyses revealed extensive intra-genomic sequence and expression consistency. Phylogenetic and comparative genomic analyses demonstrated that P. pseudocerasus was a stable autotetraploid species, closely related to wild P. pusilliflora, with the two diverging ∼18.34 million years ago. Similar to other Prunus species, P. pseudocerasus underwent a common whole-genome duplication event that occurred ∼139.96 million years ago. Because of its low fruit firmness, P. pseudocerasus is unsuitable for long-distance transportation, thereby restricting its rapid development throughout China. At the ripe fruit stage, P. pseudocerasus cv. ‘Zhuji Duanbing’ was significantly less firm than P. avium cv. ‘Heizhenzhu’. The difference in firmness is attributed to the degree of alteration in pectin, cellulose, and hemicellulose contents. In addition, comparative transcriptomic analyses identified GalAK-like and Stv1, two genes involved in pectin biosynthesis, which potentially caused the difference in firmness between ‘Zhuji Duanbing’ and ‘Heizhenzhu’. Transient transformations of PpsGalAK-like and PpsStv1 increase protopectin content and thereby enhance fruit firmness. Our study lays a solid foundation for functional genomic studies and the enhancement of important horticultural traits in Chinese cherries.

Acknowledgements

This work was funded by the China Agriculture Research System (Grant No. CARS-30-2-08), and the Natural Science Foundation of Shanghai (23ZR1430600). We thank Dr Zongyi Sun from Wuhan Grandomics Bioscience Co., Ltd for providing valuable advice.

Author contributions

C.Z. and Y.D. conceived and designed the experiments; S.J. performed the main experiments and sequencing data analysis, and drafted the manuscript; S.J. and B.C. performed the assembly and annotations; Z.L., H.L., and Y.X. measured textural variables; S.J., F.L., X.Z., and L.C. collected the samples; S.J. and Y.X. worked on the phenotyping; M.L. performed comparative transcriptomic analysis; S.J. performed X-ray micro-CT scanning; J.C. and M.X. performed visualization analysis of fruit voids; S.J. and Z.L. performed the statistical analysis; M.A.M., X.D., and S.W. participated in discussions and provided some valuable advice. All authors provided final approval for publication.

Data availability

The raw genome sequencing data of Prunus pseudocerasus are available at the National Genomics Data Center (https://ngdc.cncb.ac.cn/) under BioProject number PRJCA010538 (CRA013614). The raw read data of transcriptome sequencing were uploaded to the NCBI Sequence Read Archive (SRA) database with accession number PRJNA1041553. All data are available from the corresponding author upon request.

Supplementary data

Supplementary data are available at Horticulture Research online.

Conflict of interest

The authors declare no conflicts of interests.

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