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

AbstractBackgroundThe olive tree (Olea europaea L. subsp. europaea, Oleaceae) has been the most economic perennial crop for Mediterranean countries since its domestication around 6,000 years ago. Two taxonomic varieties are currently recognized: cultivated (var. europaea) and wild (var. sylvestris) trees. To shed light into the recent evolution and domestication of the olive tree, we sequenced the genomes of twelve individuals: ten var. europaea, one var. sylvestris, and one outgroup taxon (subsp. cuspidata). All of them were analysed together with an improved assembly of var. europaea reference genome and the available assembly of var. sylvestris.ResultsOur analyses show that cultivated olives exhibit slightly lower levels of overall genetic diversity than wild forms, and that this can be partially explained by the occurrence of a mild population bottleneck 5000-7000 years ago during the primary domestication period. We also provide the first phylogenetic analysis of genome-wide sequences, which supports a continuous process of domestication of the olive tree. This, together with population structure and introgression analyses highlights genetic admixture with wild populations across the Mediterranean Basin in the course of domestication.ConclusionsAltogether, our results suggest that a primary domestication area in the eastern Mediterranean basin was followed by numerous secondary events across most countries of southern Europe and northern Africa, often involving genetic admixture with genetically rich wild populations, particularly from the western Mediterranean Basin. Based on selection tests and a search for selective sweeps, we found that genes associated with stress response and developmental processes were positively selected in cultivars. However, we did not find evidence that genes involved in fruit size or oil content were under positive selection.

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Genomic evidence for recurrent genetic admixture during the domestication of Mediterranean olive trees (Olea europaea L.)

BMC Biology ◽

10.1186/s12915-020-00881-6 ◽

2020 ◽

Vol 18 (1) ◽

Author(s):

Irene Julca ◽

Marina Marcet-Houben ◽

Fernando Cruz ◽

Jèssica Gómez-Garrido ◽

Brandon S. Gaut ◽

...

Keyword(s):

Olea Europaea ◽

Mediterranean Basin ◽

Population Genomics ◽

Continuous Process ◽

Olive Tree ◽

Genetic Admixture ◽

Wild Populations ◽

Olea Europaea L ◽

Domestication Event ◽

Olea Europaéa

Abstract Background Olive tree (Olea europaea L. subsp. europaea, Oleaceae) has been the most emblematic perennial crop for Mediterranean countries since its domestication around 6000 years ago in the Levant. Two taxonomic varieties are currently recognized: cultivated (var. europaea) and wild (var. sylvestris) trees. However, it remains unclear whether olive cultivars derive from a single initial domestication event followed by secondary diversification, or whether cultivated lineages are the result of more than a single, independent primary domestication event. To shed light into the recent evolution and domestication of the olive tree, here we analyze a group of newly sequenced and available genomes using a phylogenomics and population genomics framework. Results We improved the assembly and annotation of the reference genome, newly sequenced the genomes of twelve individuals: ten var. europaea, one var. sylvestris, and one outgroup taxon (subsp. cuspidata)—and assembled a dataset comprising whole genome data from 46 var. europaea and 10 var. sylvestris. Phylogenomic and population structure analyses support a continuous process of olive tree domestication, involving a major domestication event, followed by recurrent independent genetic admixture events with wild populations across the Mediterranean Basin. Cultivated olives exhibit only slightly lower levels of genetic diversity than wild forms, which can be partially explained by the occurrence of a mild population bottleneck 3000–14,000 years ago during the primary domestication period, followed by recurrent introgression from wild populations. Genes associated with stress response and developmental processes were positively selected in cultivars, but we did not find evidence that genes involved in fruit size or oil content were under positive selection. This suggests that complex selective processes other than directional selection of a few genes are in place. Conclusions Altogether, our results suggest that a primary domestication area in the eastern Mediterranean basin was followed by numerous secondary events across most countries of southern Europe and northern Africa, often involving genetic admixture with genetically rich wild populations, particularly from the western Mediterranean Basin.

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Allozyme variation of oleaster populations (wild olive tree) (Olea europaea L.) in the Mediterranean Basin

Heredity ◽

10.1038/sj.hdy.6800430 ◽

2004 ◽

Vol 92 (4) ◽

pp. 343-351 ◽

Cited By ~ 82

Author(s):

R Lumaret ◽

N Ouazzani ◽

H Michaud ◽

G Vivier ◽

M-F Deguilloux ◽

...

Keyword(s):

Olea Europaea ◽

Mediterranean Basin ◽

Olive Tree ◽

Allozyme Variation ◽

Olea Europaea L ◽

Wild Olive ◽

The Mediterranean ◽

The Mediterranean Basin ◽

Olea Europaéa

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Achievements and Challenges towards a Sustainable Conservation and Use of ‘Galega vulgar’ Olea europaea Variety

Agronomy ◽

10.3390/agronomy10101467 ◽

2020 ◽

Vol 10 (10) ◽

pp. 1467

Author(s):

Hélia Sales ◽

João Nunes ◽

Maria Carlota Vaz Patto

Keyword(s):

Olive Oil ◽

Olea Europaea ◽

Production Systems ◽

Oil Quality ◽

Olive Tree ◽

Life Cycle Thinking ◽

Mediterranean Countries ◽

Sustainable Conservation ◽

Olea Europaéa

The cultivated Olea europaea L., or olive tree, is an ancient crop extremely relevant for the bioeconomy of Mediterranean countries, especially for Portugal. With orchard modernization, Portugal has the potential to become the third-largest producer of olive oil over the next decade. In this country, the main national variety is ‘Galega vulgar,’ characterized by an excellent olive oil quality, rusticity and tolerance to drought. Nevertheless, its production has suffered a reduction due to replacement by foreign varieties. The present narrative review offers an overall perspective of present gaps and challenges to the conservation and use of ‘Galega vulgar.’ Existing information about traditional and innovative olive production systems, and the importance of life cycle thinking approaches for a sustainable olive chain were synthesized, focusing particularly in the last 10 years. Furthermore, the olive molecular characterization advances and their breeding importance were also evaluated considering their application to this Portuguese variety. To ensure an efficient and sustainable exploitation of the ‘Galega vulgar,’ we propose that efforts should concentrate on the characterization of the existing variability and development of genotype to phenotype prediction tools, integrating detailed molecular marker genotypic and environmental characterization, to support better informed conservation and breeding decisions in a multi-environment context.

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Plant-parasitic nematodes associated with olive tree (Olea europaea L.) with a focus on the Mediterranean Basin: A review

Comptes Rendus Biologies ◽

10.1016/j.crvi.2014.05.006 ◽

2014 ◽

Vol 337 (7-8) ◽

pp. 423-442 ◽

Cited By ~ 25

Author(s):

Nadine Ali ◽

Elodie Chapuis ◽

Johannes Tavoillot ◽

Thierry Mateille

Keyword(s):

Olea Europaea ◽

Mediterranean Basin ◽

Olive Tree ◽

Parasitic Nematodes ◽

Plant Parasitic Nematodes ◽

Olea Europaea L ◽

The Mediterranean ◽

Plant Parasitic ◽

The Mediterranean Basin ◽

Olea Europaéa

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Metagenomic dynamics in Olea europaea after root damage and Verticillium dahliae infection

10.1101/555185 ◽

2019 ◽

Cited By ~ 1

Author(s):

Jose Manuel Martí ◽

Luis F. Arias ◽

Wladimiro Díaz ◽

Vicente Arnau ◽

Antonio Rodriguez-Franco ◽

...

Keyword(s):

Verticillium Dahliae ◽

Olea Europaea ◽

Mediterranean Basin ◽

Single Species ◽

Olive Tree ◽

Economic Damage ◽

Root Damage ◽

High Complexity ◽

The Mediterranean Basin ◽

Olea Europaéa

AbstractThe olive tree is of particular economic interest in the Mediterranean basin. Researchers have conducted several studies on one of the most devastating disorders affecting this tree, the Verticillium wilt of olive, which causes significant economic damage in numerous areas of this crop. We have analyzed the temporal metagenomic samples of a transcriptomic study in Olea europaea roots and leaves after root-damage and after a root Verticillium dahliae infection (Jimenez-Ruiz et al. 2017). Our results indicate that this infection, although led by Verticillium, is driven not by a single species but by a polymicrobial community, including their natural endophytes, which acts as a consortium in the attack to the host plant. This community includes both biotrophic and necrotrophic organisms that alternate and live together during the infection. Our results not only describe how the microbial community progresses along these processes, but also explain the high complexity of these systems, that in turn, could justify at least in part the occasional changes and disparity found at the time of classifying the kind of parasitism of a determined organism.

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Olive Leaf (Olea europaea L. folium): Potential Effects on Glycemia and Lipidemia

Annals of Nutrition and Metabolism ◽

10.1159/000505508 ◽

2020 ◽

Vol 76 (1) ◽

pp. 10-15 ◽

Cited By ~ 8

Author(s):

Nilüfer Acar-Tek ◽

Duygu Ağagündüz

Keyword(s):

Olea Europaea ◽

Olive Tree ◽

Olive Leaf ◽

Potential Health ◽

Beneficial Effects ◽

Positive Effects ◽

Olea Europaea L ◽

Toxicity Studies ◽

Mediterranean Countries ◽

Olea Europaéa

Background: Olive tree (Olea europaea, Oleaceae) leaves have been widely used in traditional herbal medicine to prevent and treat various diseases especially in Mediterranean countries. They contain several potentially bioactive compounds that may have hypoglycemic and hypolipidemic properties. Summary: The literature has recently been attempting to define the relationship between olive leaf (Olea europaea L. folium) polyphenols and a number of health problems. Oleuropein, the basic phenolic compound of olive leaf and its extract, is responsible for the characteristic bitter taste and unique aroma of olive fruits. Furthermore, it is shown that oleuropein and its hydrolyzed products have many beneficial effects on human health because of its antioxidant characters. A number of studies report that olive leaf has potentially positive effects on the parameters related to diabetes and cardiovascular diseases by various mechanisms. Besides, toxicity studies suggest that olive leaf is generally safe even at high doses. Key messages: Although current results obtained until today seem promising, the studies in this subject are usually on cell culture and animal trials. Moreover, mostly the extract forms of olive leaves are used in the studies. More randomized controlled human clinical trials with extensive toxicity studies are needed to evaluate potential health effects and safety.

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Assessment of the genetic relationship of Turkish olives (Olea europaea subsp. europaea) cultivars based on cpDNA trnL-F regions

Acta Botanica Croatica ◽

10.1515/botcro-2017-0019 ◽

2018 ◽

Vol 77 (1) ◽

pp. 88-92 ◽

Cited By ~ 2

Author(s):

Ergun Kaya ◽

Recep Vatansever ◽

Ertugrul Filiz

Keyword(s):

Genetic Relationship ◽

Olea Europaea ◽

Phylogenetic Analyses ◽

Olive Tree ◽

Sequence Length ◽

Mediterranean Countries ◽

Olive Cultivars ◽

Content Variable ◽

Relationship Of ◽

Olea Europaéa

AbstractThe olive tree (Olea europaeaL.) is one of the major cultivated species in the world, and Mediterranean countries produce about 90% of world cultivated olives. In this study, the genetic relationship of seven Turkish olive cultivars was investigated using non-codingtrnL-Fregions in chloroplastic genome. Cultivars demonstrated a similar sequence length of 330-340 bp with an average 35.26% G+C content. Variable (polymorphic/segregating), parsimony informative and total numbers of the insertion or the deletion of bases in the DNA (indel sites) were 4, 3, and 28, respectively. Nucleotide diversities π and θ were found as 0.00631 and 0.00644 respectively, while Tajima’s D was −0.786. cpDNAtrnL-Fregions of sequenced Turkish olive cultivars had a low level of genetic variations, and these non-coding regions were strictly conserved in all analyzed cultivars. Geographically distant shared more sequence similarities than relatively close cultivars. The phylogenetic analyses indicated that the biogeographic distribution of cultivars does not demonstrate any association inferring cultivar source. These results indicate the possibility of germplasm exchanges among countries or that some indel mutations contribute to variations of the Turkish olive gene pool. Thus, the authorities should develop the necessary programs to preserve the purity of native germplasms.

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Algerian Olive Germplasm and Its Relationships with the Central-Western Mediterranean Varieties Contributes to Clarify Cultivated Olive Diversification

Plants ◽

10.3390/plants10040678 ◽

2021 ◽

Vol 10 (4) ◽

pp. 678

Author(s):

Kamel Atrouz ◽

Ratiba Bousba ◽

Francesco Paolo Marra ◽

Annalisa Marchese ◽

Francesca Luisa Conforti ◽

...

Keyword(s):

Mediterranean Basin ◽

Genetic Relationships ◽

Olive Tree ◽

Mediterranean Area ◽

Western Mediterranean ◽

Central Mediterranean ◽

Western Mediterranean Basin ◽

New Information ◽

Mediterranean History ◽

New Synonymy

Olive tree with its main final product, olive oil, is an important element of Mediterranean history, considered the emblematic fruit of a civilization. Despite its wide diffusion and economic and cultural importance, its evolutionary and phylogenetic history is still difficult to clarify. As part of the Mediterranean basin, Algeria was indicated as a secondary diversification center. However, genetic characterization studies from Maghreb area, are currently underrepresented. In this context, we characterized 119 endemic Algerian accessions by using 12 microsatellite markers with the main goal to evaluate the genetic diversity and population structure. In order to provide new insights about the history of olive diversification events in the Central-Western Mediterranean basin, we included and analyzed a sample of 103 Italian accessions from Sicily and, a set of molecular profiles of cultivars from the Central-Western Mediterranean area. The phylogenetic investigation let us to evaluate genetic relationships among Central-Mediterranean basin olive germplasm, highlight new synonymy cases to support the importance of vegetative propagation in the cultivated olive diffusion and consolidate the hypothesis of more recent admixture events occurrence. This work provided new information about Algerian germplasm biodiversity and contributed to clarify olive diversification process.

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