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.

Plant growth-promoting rhizobacteria (PGPR) can rebalance growth–defense trade-offs in plants. However, the temporal molecular mechanisms underlying sustained growth promotion in woody fruit crops, particularly cherry (Prunus avium), remain largely unclear. This study inoculated Gisela 6 sweet cherry seedlings with three PGPR strains (Rahnella Y17, Arthrobacter Y37, and Bacillus megaterium P6). Phenotypic and physiological traits were assessed at 60 days (d), while targeted phytohormone metabolomics and root transcriptomes were profiled at 30 and 40 d post-treatment. Our results demonstrated that all three PGPR strains enhanced plant growth, photosynthetic capacity, and root architecture, with Y37 demonstrating superior biomass promotion. Phytohormone dynamics featured consistent ABA (abscisic acid) suppression, coupled with an early elevation of GA (gibberellin) and auxin followed by subsequent cytokinin accumulation. Notably, Y37 uniquely enriched jasmonate intermediates. Comparative transcriptomic analysis uncovered strain-specific trajectories, with integrated co-expression analysis defining modules associated with early metabolism and later structural remodeling. Key hub genes were identified as involved in hormone regulation and cell wall synthesis. Collectively, these findings suggest that Y37 drives a temporal partitioning from metabolic priming to architectural reinforcement by reallocating carbon and tuning hormone pathways, thereby underpinning superior growth and resilience. This study provides novel insights into PGPR-based strategies for sustainable cherry production.

Exogenous glucose functions not only as a carbon source but also as a key signaling molecule involved in regulating root development and metabolism in plants. To elucidate the molecular mechanisms underlying this response in cherry rootstock (Prunus cerasus), we performed RNA-seq on lateral roots collected at 0, 6, 12, 24, 48, and 72 h after glucose treatment. Transcriptome profiling revealed a dynamic and sustained transcriptional reprogramming, with a total of 461 differentially expressed genes (DEGs) consistently altered across all post-treatment time points relative to the control (T0). Weighted gene co-expression network analysis identified five modules strongly correlated with glucose exposure, notably enriched for genes involved in nitrogen, carbon, and sulfur metabolism. Functional enrichment analyses further revealed a pronounced overrepresentation of pathways associated with nutrient utilization, as well as carbon fixation, glycolysis, amino acid biosynthesis, and stress-responsive processes such as glutathione metabolism and MAPK signaling. Intriguingly, key transcription factors and signaling components were consistently co-enriched across multiple functional categories, suggesting the presence of a tightly coordinated regulatory network that links sugar sensing to metabolic reprogramming, redox homeostasis, and developmental plasticity. Notably, glucose treatment induced both activation and repression of nitrogen-related genes in distinct co-expression modules, indicating fine-tuned modulation of nutrient uptake in response to carbon availability. Together, these findings suggest that exogenous glucose triggers a systems-level shift in root physiology, coordinating primary metabolism with stress adaptation and growth regulation through tightly interconnected carbon–nitrogen–sulfur metabolic circuits.