Combining a high-caliber chromosome-level genome and root single-cell atlas resolves genetic diversity and root development in <i>Olea europaea</i> subsp. <i>cuspidata</i>

Olea europaea subsp. cuspidata, a subspecies of olive trees, stands out for its remarkable stress tolerance and commonly serves as a rootstock that enhances olive oil yield. To explore its genomic and cellular underpinnings for potential breeding applications, a chromosome-scale genome assembly and a root-specific single-cell atlas of O. europaea subsp. cuspidata was resolved. Using a combined survey evaluation strategy along with PacBio CLR and Hi-C sequencing technologies, a total genome of 1.62 Gb was obtained (23 chromosomes; N50: 55.72 Mb). Phylogenetic analysis revealed that Oleaceae plants diverged by approximately 17.2 Mya, with O. europaea subsp. cuspidata splitting from other O. europaea lineages at approximately 5.7 Mya. It is genetically closer to the cultivated olive O. europaea subsp. europaea cv. 'Arbequina' than to the wild olive O. europaea subsp. europaea var. sylvestris. Additionally, a dynamic molecular map of olive roots was generated at single-cell resolution to reconstruct the continuous root cell differentiation and developmental trajectory. This helps to unravel key regulatory genes in olive root development and adaptation to the external environment. This study explored the diversity of olive trees at genomic and root cellular levels, with insights to support the theoretical basis for enhanced stress tolerance, aiding the global introduction and promotion of olive trees.