Phylogenomics of the olive tree (Olea europaea) reveals the relative contribution of ancient allo- and autopolyploidization events

Background: Polyploidization is one of the major evolutionary processes that shape eukaryotic genomes, being particularly common in plants. Polyploids can arise through direct genome doubling within a species (autopolyploidization) or through the merging of genomes from distinct species after hybridization (allopolyploidization). The relative contribution of both mechanisms in plant evolution is debated. Here we used phylogenomics to dissect the tempo and mode of duplications in the genome of the olive tree (Olea europaea), one of the first domesticated Mediterranean fruit trees. Results: Our results depict a complex scenario involving at least three past polyploidization events, of which two—at the bases of the family Oleaceae and the tribe Oleeae, respectively—are likely to be the result of ancient allopolyploidization. A more recent polyploidization involves specifically the olive tree and relatives. Conclusion: Our results show the power of phylogenomics to distinguish between allo- and auto polyploidization events and clarify the contributions of duplications in the evolutionary history of the olive tree.TG’s group acknowledges support from the Spanish Ministry of Economy and Competitiveness through grants “Centro de Excelencia Severo Ochoa 2013-2017” SEV-2012-0208 and BFU2015-67107, cofounded by the European Regional Development Fund; from the Catalan Research Agency (AGAUR) SGR857, from the CERCA programme/ Generalitat de Catalunya; and from the European Union’s Horizon 2020 research and innovation program under Marie Sklodowska-Curie grant agreement H2020-MSCA-ITN-2014-642095 and European Research Council grant agreement ERC-2016-CoG-724173. TG and PV acknowledge support from Banco Santander for the olive genome sequencing project. IJ was supported in part by a grant from the Peruvian Ministry of Education, “Beca Presidente de la República” (2013-III)