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

Chinese cherry () 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 was a stable autotetraploid species, closely related to wild , with the two diverging ~18.34 million years ago. Similar to other species, underwent a common whole-genome duplication event that occurred ~139.96 million years ago. Because of its low fruit firmness, is unsuitable for long-distance transportation, thereby restricting its rapid development throughout China. At the ripe fruit stage, cv. 'Zhuji Duanbing' was significantly less firm than 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 - and , two genes involved in pectin biosynthesis, which potentially caused the difference in firmness between 'Zhuji Duanbing' and 'Heizhenzhu'. Transient transformations of and 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.