High-Quality Genome Assembly of subsp. Provides Insights Into Its Resistance to Fungal Diseases in the Summer Rain Belt in East Asia.

The olive tree ( L.) is the most iconic fruit crop of the Mediterranean Basin. Since the plant was introduced to China in the 1960s, the summer rain climate makes it susceptible to pathogens, leading to some olive diseases. L. subsp. is natively distributed in the Yunnan province of China. It has a smaller fruit size, lower oil content, and higher resistance compared to subsp. , which makes subsp. a critical germplasm resource to be investigated. Here, a high-quality genome of subsp. with 1.38 Gb in size was assembled and anchored onto 23 pseudochromosomes with a mounting rate of 85.57%. It represents 96.6% completeness [benchmarking universal single-copy orthologs (BUSCO)] with a contig N50 of 14.72 Mb and a scaffold N50 of 52.68 Mb, which shows a significant improvement compared with other olive genomes assembled. The evaluation of the genome assembly showed that 92.31% of resequencing reads and an average of 96.52% of assembled transcripts could be aligned to the assembled genome. We found that a positively selected gene, , was shared with the results of transcriptome analysis. This gene belongs to the susceptible gene and negatively regulates the disease resistance process. Furthermore, we identified the genus which causes the leaf spot disease in the infected leaves. The high-quality chromosome-level genomic information presented here may facilitate the conservation and utilization of germplasm resources of this subspecies and provide an essential genetic basis for further research into the differences in oil content and resistance between subsp. and .