Genome sequence of the olive tree, Olea europaea

Abstract

BackgroundThe Mediterranean olive tree (Olea europaea subsp. europaea) was one of the first trees to be domesticated and is currently of major agricultural importance in the Mediterranean region as the source of olive oil. The molecular bases underlying the phenotypic differences among domesticated cultivars, or between domesticated olive trees and their wild relatives, remain poorly understood. Both wild and cultivated olive trees have 46 chromosomes (2n).FindingsA total of 543 Gb of raw DNA sequence from whole genome shotgun sequencing, and a fosmid library containing 155,000 clones from a 1,000+ year-old olive tree (cv. Farga) were generated by Illumina sequencing using different combinations of mate-pair and pair-end libraries. Assembly gave a final genome with a scaffold N50 of 443 kb, and a total length of 1.31 Gb, which represents 95 % of the estimated genome length (1.38 Gb). In addition, the associated fungus Aureobasidiumpullulans was partially sequenced. Genome annotation, assisted by RNA sequencing from leaf, root, and fruit tissues at various stages, resulted in 56,349 unique protein coding genes, suggesting recent genomic expansion. Genome completeness, as estimated using the CEGMA pipeline, reached 98.79 %.ConclusionsThe assembled draft genome of O. europaea will provide a valuable resource for the study of the evolution and domestication processes of this important tree, and allow determination of the genetic bases of key phenotypic traits. Moreover, it will enhance breeding programs and the formation of new varieties.

Genome of wild olive and the evolution of oil biosynthesis

“…About 51% of the genome assembly was found to be composed of repetitive DNA (Fig. 1), which is less than what was found for the draft genome of a recently published cultivated olive tree (63%) (12). Genome comparisons between oleaster and nine other plant species showed differences in gene numbers, transcript lengths and proportions of transposable elements (TEs; SI Appendix, Table S5b).…”

“…Leccino (13) and O. europaea cv. Farga (12), at ~4x and ~150x coverage, respectively. The latter, with a size of 1.31 Gbp, was preliminary annotated solely by utilizing RNA sequencing (RNA-seq) data, which resulted in more than 56,000 protein-coding genes (12).…”

“…Farga (12), at ~4x and ~150x coverage, respectively. The latter, with a size of 1.31 Gbp, was preliminary annotated solely by utilizing RNA sequencing (RNA-seq) data, which resulted in more than 56,000 protein-coding genes (12). Compared to the oleaster genome presented here, the cultivated olive tree has a smaller genome size, albeit with a higher number of genes.…”

Selective Amplification of Start codon Polymorphic Loci (SASPL): a new PCR-based molecular marker in olive

“…Olive is a diploid (2n = 46) with a genome size of 1.38 Gb (Cruz et al, 2016) and about 47 % of its unigenes are shared with Vitis vinifera (Muleo et al, 2012). The full genome of olive (Cruz et al, 2016) was used as template for the in silico PCR analysis against all studied PCR primers (83 primers) to reveal the possible PCR amplimers.…”

“…The full genome of olive (Cruz et al, 2016) was used as template for the in silico PCR analysis against all studied PCR primers (83 primers) to reveal the possible PCR amplimers. Practical Extracting and Reporting Language (PERL) scripts were used for performing the in silico PCR analysis by the following criteria: the maximum length of produced amplimer ≤ 1500 bp and the minimum length ≥ 50.In addition, the maximum acceptable sequence mismatch between the primer and the DNA template for SCoT ≤ 4 bp, RAPD ≤ 1bp, SAMPL ≤ 0bp and SASPL ≤ 4bp.…”