PacBio genome assembly of <i>Olea europaea</i> L. subsp. <i>europaea</i> cultivars ‘Frantoio’ and ‘Leccino’ reveal main structural differences in key genes related to salt stress

Abstract We present two high-quality genome assemblies for Olea europaea L. cultivars ‘Frantoio’ and ‘Leccino’ leveraging PacBio HiFi sequencing to achieve approximately 30× genome coverage for each cultivar. The assemblies span 1.18 Gbp and 1.43 Gbp with contig N50 values of 1.78 Mbp and 45.88 Mbp for ‘Frantoio’ and ‘Leccino’ respectively. BUSCO analysis revealed a great genome completeness (∼97.9%), surpassing many of earlier Olea europaea assemblies and is in par with the most recent one. Repetitive content accounted for ∼67.5% in ‘Frantoio’ and ∼70.8% in ‘Leccino’ with long terminal repeats (LTRs) dominating. Notably, a tandem repeat family, Satellite 1, represented ∼16.9% and ∼8.6% of the ‘Leccino’ and ‘Frantoio’ genomes, respectively. The structural variant (SV) analysis was done with a particular focus on those associated with nine key gene families involved in salinity tolerance and identified cultivar-specific genomic differences, emphasizing the diversity within domesticated olives. This comprehensive analysis provides valuable resources for studying olive genome evolution, domestication, and genetic improvement, underscoring the utility of long-read sequencing for resolving complex genomic features.