Lessons From Whole Genome Sequencing of Olive Tree (Olea europaea L.)

The olive tree (Olea europaea L.) is an economically-important fruit tree, being widely spread in the Mediterranean Basin. It is one of the most-important oil crops in the world, belonging to the family of Oleaceae, order of Lamiales, which includes important members for their essential oils, fragrances and phenolics. Olive tree is a diploid (2n = 2x = 46), predominantly allogamous, and vegetatively propagated species. To date, there is no available genome-level sequence data of olive tree. The wild olive tree (O. europaea var. sylvestris) genome was sequenced and assembled with 246X coverage. SOAPdenovo was used to assemble reads, which resulted in a draft genome of 1.48 Gb with scaffold N50 of 228 kb, which is near to previous estimates by flow cytometry and k-mer analyses (~1.46 Gb). A total of 42,843 scaffolds (>1 kb) were assembled with about 80% of the total assembly (1.14 Gb). Using a newly-constructed genetic map, 50% of the sequences were anchored into 23 linkage groups, which included 572 Mb. About 50% of the total genome assembly was found to be composed of repetitive DNA. Transposable elements and interspersed repeats occupied ~43% of the genome. Protein-encoding gene models were constructed by combined methodology, including de novo, homology-based and RNA-Seq-aided predictions. A total of 50,684 protein-encoding gene models were predicted for total assembly, of which 31,245 were anchored into chromosomes. To estimate heterozygosity in the genome, a k-mer distribution approach was performed, showing a distribution of about 1.3%. A phylogenetic tree was constructed for evolutionary analyses, on the basis of a concatenated sequence-alignment of the 99 single copy genes shared by olive tree and other 12 plant species. In this phylogenetic dendrogram, the olive tree clustered with oil-crop sesame. Whole-genome duplication and speciation events were analyzed, via fourfold synonymous third-codon transversion (4DTv) approach, showing that there was a recent whole-genome duplication event in the olive tree, after speciation from sesame. The olive tree genome was also subjected to synteny analyses with sesame, resulting in 1,727 synteny blocks. Genes involved in oil biosynthesis, ripening, secondary metabolite synthesis and alternate bearing, as well as small RNAs and transcription factor genes were annotated and further analyzed, using transcriptome data from several tissues. The olive tree reference genome will serve as a crucial source not only for the study of olive tree genome biology, but also for tree genomics, further facilitating more effective olive tree breeding programs.