The De Novo Genome Assembly of Olea europaea subsp. cuspidate , a Widely Distributed Olive Close Relative.

The olive complex, comprising six subspecies, is a valuable plant for global trade, human health, and food safety. However, only one subspecies ( subsp. , OE) and its wild relative ( subsp var, 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, subsp. (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 genome assembly and protein-coding gene pool for subsp. (OC) in this study, which may facilitate breeding applications of improved olive varieties from this widely distributed olive close relative.