Genome sequencing of wild and cultivated mediterranean olive trees (Olea europaea) identifies recurrent hybridization during domestication. Olice cultivars resequencing

The olive tree (Olea europaea L. subsp. europaea, Oleaceae) is an iconic plant of the Mediterranean region. This small tree has been cultivated for 6,000 years for its wood and fruits, which are consumed as table olives or used to produce oil. Currently, the olive tree is an important economic perennial crop for the Mediterranean countries. Two taxonomic olive tree varieties are recognized, which correspond to cultivated (europaea) and wild forms (sylvestris). To shed light into the recent evolution and domestication of the olive tree, we sequenced the whole genome of twelve individuals: ten europaea, one sylvestris, and one outgroup of the subsp. cuspidata, which we analysed together with two available reference genome assemblies (one var. europaea and one sylvestris). Our analyses show that cultivated olives exhibit slightly lower levels of genetic diversity than wild forms, and that this can be partially explained by a mild population bottleneck occurred 5000-7000 years ago during the primary domestication period. Phylogenetic, population structure, and introgression analyses support a continuous process of domestication in olive, and highlight genetic admixture with wild populations across the Mediterranean Basin as a common and relevant process. Altogether, our results suggest that a primary domestication in the eastern Mediterranean basin, was followed by numerous secondary events in most countries of southern Europe and northern Africa often involving genetic admixture with genetically rich wild populations, particularly from the western Mediterranean Basin. Based on selection tests and a search for selective sweeps, we found that genes associated with stress response and developmental processes were positively selected in cultivars. However, we did not find evidence that genes involved in fruit size or oil content were under positive selection.