De novo Whole Genome Sequencing of Olive Tree (Olea europaea L.)

Olive (Olea europaea L.) is an economically important fruit tree, being widely spread in the Mediterranean Basin. The olive tree 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. We have sequenced and assembled the genome of wild olive tree (O. europaea var. sylvestris) with coverage of 246X. SOAPdenovo was used to assemble the genome, 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). We assembled 42,843 scaffolds (>1 kb) with about 80% of the total assembly (1.16 Gb). Using a newly constructed genetic map we anchored 50% of the sequences 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 47% 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 60,214 protein-encoding gene models were predicted for total assembly, of which 36,381 were anchored into chromosomes. To estimate level of heterozygosity in the genome, we performed k-mer distribution approach and found that the distribution is 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 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, before speciation from sesame. The olive tree genome was also subjected to synteny analyses with sesame, resulting in 1,727 synteny blocks. We annotated and further analyzed genes involved in oil biosynthesis, ripening, secondary metabolite synthesis, and alternate bearing as well as small RNAs and transcription factor genes using transcriptome data from several tissues. The olive reference genome sequence will serve as a crucial source not only for the study of olive genome biology but also for tree genomics and will facilitate more effective olive breeding programs.