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

Abstract

BackgroundPolyploidization 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.ResultsOur 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.ConclusionOur 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.Electronic supplementary materialThe online version of this article (10.1186/s12915-018-0482-y) contains supplementary material, which is available to authorized users.

Genomic evidence for recurrent genetic admixture during domestication mediterranean olive trees (Olea europaea)

“…In addition, we produced individual annotated assemblies for the plastid and mitochondrial genomes, which were not provided as separate assemblies in earlier releases. Our comparison of our improved nuclear assembly with the recently released assembly of an oleaster from Turkey (23) and the identification of shared duplicated regions provides additional support to the previously proposed ancient polyploidization in olives (25). Unexpectedly, we found apparent differences in gene content even using a conservative approach that is independent of differences in annotation methodologies.…”

“…The comparison between both assemblies (Additional file 1: Fig. S1b) shows a high level of conserved synteny and confirms the ancient polyploidization event in O. europaea described earlier (25) as many regions appear duplicated between the two genomes.…”

“…Previous phylogenetic analyses have suggested the existence of ancestral inter-subspecies hybridization in deep nodes of the evolutionary tree of O. europaea (25). Our population genomics results discussed above and a recently published transcriptome-based population analysis (11) suggest recent intraspecific genetic admixture between western cultivars and western sylvestris.…”

Phylogenomics using low‐depth whole genome sequencing: A case study with the olive tribe

“…The topological incongruence between the phylogenies obtained with the two whole reference genomes, both of which are fragmented, might stem from the high number of closely related duplicates in the olive tree genome, either due to a recent polyploidization (Julca et al, ) or failure to collapse divergent alleles in the genome assembly (Hahn, Zhang, & Moyle, ; Pryszcz & Gabaldón, ). The latter hypothesis can be argued for because the basic chromosome number ( n = 23; Taylor, ) is stable in Oleeae and the sequenced olive cultivar (“Farga”; Cruz et al, ) is highly heterozygous due to recent admixture between distinct gene pools (Besnard et al, ; Diez et al, ).…”

“…Neither of these genomes is assembled to the chromosome level, and they therefore consist of a collection of contigs and scaffolds. The olive genome includes recently diverged copies of many genes, which has been interpreted as the remnants of a recent polyploidization event followed by a rapid rediploidization (Julca, Marcet‐Houben, Vargas, & Gabaldón, ). However, these duplicated regions could also be an assembly artefact in which divergent alleles have not been merged due to the high heterozygosity of the olive cultivar “Farga” (Besnard et al, ; Cruz et al, ; Diez et al, ).…”