The olive complex, comprising six subspecies, is a valuable plant for global trade, human health, and food safety. However, only one subspecies (Olea europaea subsp. europaea, OE) and its wild relative (Olea europaea subsp. europaea var. sylvestris, OS) have genomic references, hindering our understanding of the evolution of this species. Using a hybrid approach by incorporating Illumina, MGI, Nanopore, and Hi-C technologies, we obtained a 1.20-Gb genome assembly for the olive subspecies, Olea europaea subsp. cuspidate (OC), with contig and scaffold N50 values of 5.33 and 50.46 Mb, respectively. A total of 43,511 protein-coding genes were predicted from the genome. Interestingly, we observed a large region (37.5 Mb) of “gene-desert” also called “LTR-hotspot” on chromosome 17. The gene origination analyses revealed a substantial outburst (19.5%) of gene transposition events in the common ancestor of olive subspecies, suggesting the importance of olive speciation in shaping the new gene evolution of OC subspecies. The divergence time between OC and the last common ancestor of OE and OS was estimated to be 4.39 Mya (95% CI: 2.58–6.23 Mya). The pathways of positively selected genes of OC are related to the metabolism of cofactors and vitamins, indicating the potential medical and economic values of OC for further research and utilization. In summary, we constructed the de novo genome assembly and protein-coding gene pool for Olea europaea subsp. cuspidate (OC) in this study, which may facilitate breeding applications of improved olive varieties from this widely distributed olive close relative.

A reasonable branch bending angle is essential for optimizing canopy structure and regulating metabolic distribution in fruit trees. ‘Jinyefoxilan’ is a new olive variety bred by crossing ‘Frantoio’ and Olea cuspidata Wall., characterized by rapid growth and high oil concentration. This study evaluated the physiological and metabolic responses of ‘Jinyefoxilan’ to natural growth (CK), 60°, 90°, and 110° bending. Parameters including leaf morphology, photosynthetic pigments, endogenous hormones, mineral distribution, and fruit quality were analyzed. The results demonstrated that the 60° treatment stimulated leaf gibberellin synthesis. The 90° treatment facilitated the synergistic enrichment of nitrogen and potassium in leaves, resulting in the highest fruit oil concentration, although the yield per plant was the lowest among all treatments. Conversely, 110° bending significantly altered the endogenous hormonal balance, with indole-3-acetic acid concentration reaching 13.3 times that of the CK. This treatment achieved the numerically highest fruit set rate and yield per plant, accompanied by significant accumulations of calcium, magnesium, and phosphorus. However, the 110° angle also induced severe N and K deficits, resulting in the lowest fruit moisture and oil concentration. In conclusion, 90° branch bending represents the optimal strategy for enhancing intrinsic fruit quality and oil accumulation. Although 110° bending maximizes yield, it necessitates supplemental potassium fertilization during fruit development to mitigate metabolic limitations. These findings provide a theoretical and practical basis for canopy management and cultivation of ‘Jinyefoxilan’ olives.