How to Choose a Good Marker to Analyze the Olive Germplasm (Olea europaea L.) and Derived Products.

The olive tree (Olea europaea L.) is one of the most cultivated crops in the Mediterranean basin. Its economic importance is mainly due to the intense production of table olives and oil. Cultivated varieties are characterized by high morphological and genetic variability and present a large number of synonyms and homonyms. This necessitates the introduction of a rapid and accurate system for varietal identification. In the past, the recognition of olive cultivars was based solely on analysis of the morphological traits, however, these are highly influenced by environmental conditions. Therefore, over the years, several methods based on DNA analysis were developed, allowing a more accurate and reliable varietal identification. This review aims to investigate the evolving history of olive tree characterization approaches, starting from the earlier morphological methods to the latest technologies based on molecular markers, focusing on the main applications of each approach. Furthermore, we discuss the impact of the advent of next generation sequencing and the recent sequencing of the olive genome on the strategies used for the development of new molecular markers.

On the Squalene Content of CV Chondrolia Chalkidikis and Chalkidiki (Greece) Virgin Olive Oil.

This work is a continuation of efforts to establish the nutritional profile of virgin olive oil (VOO) from cv. Chondrolia Chalkidikis and Chalkidiki and to strengthen its positioning in the global VOO landscape. VOOs produced at an industrial scale in different olive mills of the Chalkidiki (Greece) regional unit as well as VOOs obtained at the laboratory scale from drupes of different maturity stages for four consecutive harvesting years were examined for their squalene (SQ) content using both HPLC and GC procedures. The mean values of SQ were found to be 4228 (HPLC) and 4865 (GC) mg/kg oil (n = 15) and were of the same magnitude as that in VOOs from cv Koroneiki (4134 mg/kg, n = 23). Storage of VOOs in the dark at room temperature for 18 months indicated an insignificant mean SQ content loss (~2%) in comparison to a mean loss of 26% for alpha-tocopherol content. This finding strengthens our view that SQ does not act as a radical scavenger that donates hydrogen atoms to the latter. The four consecutive harvest years studied indicated a clear declining trend in VOO SQ concentration upon olive ripening. To our knowledge, this is the first systematic work concerning the SQ content of Chondrolia Chalkidikis and Chalkidiki VOOs.

Essential Oil Volatile Fingerprint Differentiates Croatian cv. Oblica from Other Olea europaea L. Cultivars.

Olive leaves are a highly available by-product from table olive and olive oil production. They are nowadays strongly valuable for their major bioactive compounds and their beneficial effects. To determine the differences between two Croatian domestic (Lastovka, Oblica) and two introduced (Leccino, Frantoio) cultivars, physical and chemical analysis of olive leaves were performed: surface area, color variability, total phenolic amounts, and essential oil volatile profiles were analyzed at three harvest periods. All cultivars greatly differed in surface area, with cv. Lastovka being the smallest. Color variability resulted in an overall decrease in darkness and amounts of green and yellow that could be attributed to a decrease in photosynthetic demand and chlorophyll content. The highest amount of total phenolic content occurred in the summer months, followed by a reduction until October. Essential oils volatiles were determined by GC-MS and showed great diversity not only amongst cultivars but also between harvest periods, with overall 45 compounds identified. Principal component analysis distinguished domestic cultivar Oblica from the other observed cultivars, mainly due to its essential oil volatile fingerprint. Compounds that differentiated cv. Oblica were aldehydes ((E,Z)-2,4-heptadienal, (E,E)-2,4-heptadienal, decanal), ketones ((E)-ß-damascone, dihydrodehydro-ß-ionone), sesquiterpenes (cyclosativene, α-copaene, α-muurolene) and saturated hydrocarbons (tetradecane, hexadecane). Essential oil volatile fingerprint attributed the highest to the biodiversity of domestic cv. Oblica through all three harvest periods.

Study of the olive ß-glucosidase gene family putatively involved in the synthesis of phenolic compounds of virgin olive oil.

BACKGROUND: Hydrolysis of the fruit phenolic glucosides occurring during the oil extraction process is the main biochemical reaction affecting the biosynthesis and accumulation of secoiridoid compounds in virgin olive oil. An integrated approach at the molecular, biochemical, and metabolic level was used to study the olive ß-glucosidase gene family in seven olive cultivars selected by their different phenolic profiles. RESULTS: Eight ß-glucosidase genes have been identified by in silico analysis of an olive transcriptome. Their expression levels were analyzed by reverse transcription quantitative polymerase chain reaction in olive fruits at different ripening stages: I, green fruits, 16-19 weeks after flowering (WAF); II, yellow-green fruits, 22-25 WAF; III, turning fruits, 28-31 WAF; and IV, fully ripe fruits, 35-40 WAF. Gene expression was compared with the level of ß-glucosidase activity in the fruit and with the phenolic composition of fruits and oils from different olive cultivars. Phylogenetic analysis of the encoded proteins and differences found among the ß-glucosidase genes based on Gene Ontology enrichment analysis data suggests maximum involvement of two genes, OeBGLU1A and OeBGLU1B, in the phenolic composition of virgin olive oil. Positive correlation coefficients were found within each olive cultivar between OeBGLU1A and OeBGLU1B gene expression data and the phenolic content of the oil. CONCLUSION: The results obtained suggest that the expression pattern of specific ß-glucosidase genes may be an accurate predictor for the phenolic content of virgin olive oil that could be used in olive breeding programs. © 2021 Society of Chemical Industry.

Genetic Structure and Core Collection of Olive Germplasm from Albania Revealed by Microsatellite Markers.

Olive is considered one of the oldest and the most important cultivated fruit trees in Albania. In the present study, the genetic diversity and structure of Albanian olive germplasm is represented by a set of 194 olive genotypes collected in-situ in their natural ecosystems and in the ex-situ collection. The study was conducted using 26 microsatellite markers (14 genomic SSR and 12 Expressed Sequence Tag microsatellites). The identity analysis revealed 183 unique genotypes. Genetic distance-based and model-based Bayesian analyses were used to investigate the genetic diversity, relatedness, and the partitioning of the genetic variability among the Albanian olive germplasm. The genetic distance-based analysis grouped olives into 12 clusters, with an average similarity of 50.9%. Albanian native olives clustered in one main group separated from introduced foreign cultivars, which was also supported by Principal Coordinate Analysis (PCoA) and model-based methods. A core collection of 57 genotypes representing all allelic richness found in Albanian germplasm was developed for the first time. Herein, we report the first extended genetic characterization and structure of olive germplasm in Albania. The findings suggest that Albanian olive germplasm is a unique gene pool and provides an interesting genetic basis for breeding programs.

Characterization of virgin olive oils from Spanish olive varieties introduced in Mendoza, Argentina, and their comparison with the autochthonous variety.

BACKGROUND: The aim of this work was to evaluate and compare oil production and its quality in three Spanish olive varieties (Genovesa, Villalonga, and Nevadillo blanco) growing outside the Mediterranean basin with the Argentine autochthonous variety (Arauco). Fruit parameters and oil characteristics were evaluated using samples collected from the germplasm collection of Mendoza province and elaborated in the same place. RESULTS: The levels of phenolic compounds and the fatty acid composition of the samples were comparable with those previously published for these Spanish varieties, grown in the Mediterranean basin, showing the adaptability of olive trees. Observing the levels of phenolic compounds and oxidative stability, a strong correlation between oxidative stability and oleocanthal was observed. CONCLUSION: The characteristics of the fruit and oil differed according to variety and season. The inter-harvest stability was different depending on the variety. Genovesa was observed to be the most stable variety according to its fruit and oil characteristics - even more stable than the autochthonous variety, Arauco. However, in terms of the composition of phenolic compounds, Arauco was the most stable between harvests, this characteristic being more important for the taste and uniformity of the product. © 2020 Society of Chemical Industry.

Chloroplast Genome Variation and Evolutionary Analysis of Olea europaea L.

Olive (Olea europaea L.) is a very important woody tree and favored by consumers because of the fruit's high-quality olive oil. Chloroplast genome analysis will provide insights into the chloroplast variation and genetic evolution of olives. The complete chloroplast genomes of three accessions (O. europaea subsp. cuspidata isolate Yunnan, O. europaea subsp. europaea var. sylvestris, and O. europaea subsp. europaea var. frantoio) were obtained by next-generation sequencing technology. A total of 133 coding regions were identified in the three chloroplast genomes without rearrangement. O. europaea subsp. europaea var. sylvestris and O. europaea subsp. europaea var. frantoio had the same sequences (155,886 bp), while O. europaea subsp. cuspidata isolate Yunnan (155,531 bp) presented a large gap between rps16 and trnQ-UUG genes with six small gaps and fewer microsatellites. The whole chloroplast genomes of 11 O. europaea were divided into two main groups by a phylogenetic tree and O. europaea subsp. cuspidata formed a separate group (Cuspidata group) with the other subspecies (Mediterranean/North African group). Identification of consistency and diversity among O. europaea subspecies will benefit the exploration of domestication events and facilitate molecular-assisted breeding for O. europaea.

EST-SNP Study of Olea europaea L. Uncovers Functional Polymorphisms between Cultivated and Wild Olives.

BACKGROUND: The species Olea europaea includes cultivated varieties (subsp. europaea var. europaea), wild plants (subsp. europaea var. sylvestris), and five other subspecies spread over almost all continents. Single nucleotide polymorphisms in the expressed sequence tag able to underline intra-species differentiation are not yet identified, beyond a few plastidial markers. METHODS: In the present work, more than 1000 transcript-specific SNP markers obtained by the genotyping of 260 individuals were studied. These genotypes included cultivated, oleasters, and samples of subspecies guanchica, and were analyzed in silico, in order to identify polymorphisms on key genes distinguishing different Olea europaea forms. RESULTS: Phylogeny inference and principal coordinate analysis allowed to detect two distinct clusters, clearly separating wilds and guanchica samples from cultivated olives, meanwhile the structure analysis made possible to differentiate these three groups. Sequences carrying the polymorphisms that distinguished wild and cultivated olives were analyzed and annotated, allowing to identify 124 candidate genes that have a functional role in flower development, stress response, or involvement in important metabolic pathways. Signatures of selection that occurred during olive domestication, were detected and reported. CONCLUSION: This deep EST-SNP analysis provided important information on the genetic and genomic diversity of the olive complex, opening new opportunities to detect gene polymorphisms with potential functional and evolutionary roles, and to apply them in genomics-assisted breeding, highlighting the importance of olive germplasm conservation.

Evolution of Phenotypic Traits and Main Functional Components in the Fruit of 'Chenggu-32' Olives (Olea europaea L.) Cultivated in Longnan (China).

China has taken olive cultivation as a significant part of its agricultural development. Longnan city of Gansu province was marked into the world olive distribution map by International Olive Oil Council in 1998. However, so far, little research has been done on the growth and development stages of Chinese olives. The objective of this study was to investigate the dynamics changes of several quality characteristics of olive oil at different sampling times. Olive fruit of 'Chenggu-32' grown in Longnan were harvested at twenty-four time periods and used for determination of phenotypic traits and oil quality characteristics: total polyphenols and flavonoids contents, as well as fatty acid composition by using Gas Chromatography-Mass Spectrometer (GC-MS) and analysed by using Principal Components Analysis (PCA). Towards maturation, fruit moisture content decreased while oil content increased. Levels of both total flavonoids and total polyphenols contents slightly decreased first then increased. The ratio of unsaturated to saturated fatty acids was close to three. The ratio of monounsaturated fatty acids (MUFA)/ polyunsaturated fatty acids (PUFA) was from 2.28 to 4.05. The oleic acid (C18:1)/linoleic acid (C18:2) ratio was varied between 5.23 and 10.67 according to different sampling dates. The olive oil had lower oleic acid (C18:1) levels, higher linoleic acid (C18:2), linolenic acid (C18:3), and palmitic acid (C16:0) levels compared to Codex values (2017) in some periods, which is the characteristics fatty acid composition of 'Chenggu-32' variety in Longnan, China.

Advances in biocultural geography of olive tree (Olea europaea L.) landscapes by merging biological and historical assays.

Olive tree is a vector of cultural heritage in Mediterranean. This study explored the biocultural geography of extra virgin olive oil (EVOO) from the cultivar Ogliarola campana in Campania region, Italy. Here, the rich cultural elements related to olive tree and oil represent a suitable case study for a biocultural analysis. We joined analytical techniques, based on stable isotopes and trace elements of EVOOs, with humanistic analyses, based on toponymy and historical data. In order to provide a science-based assessment of the terroir concept, we set up a new method of data analysis that inputs heterogeneous data from analytical and anthropic variables and outputs an original global evaluation score, named terroir score, as a measure of biocultural distinctiveness of the production areas. The analysis highlighted two distinct cultural sub-regions in the production area of Ogliarola campana: a continental cluster in the inner area of Irpinia and a coastal one around Salerno province. Finally, a biocultural map displays the diversity of heterogeneous variables and may support science-based decision making for territory valorisation. This novel biocultural analysis is a promising approach to substantiate the terroir concept with science-based elements and appears suitable to characterize local agri-food products with old tradition and historical data.

Varietal Effect on the Concentration and Anti-Inflammatory Activity of Hydroxytyrosol in French Olive Oils.

Numerous studies have been carried out on the bioactive properties of hydroxytyrosol (HT) in olive oils (OOs), although there are few reports comparing anti-inflammatory activity among different olive varieties or regions of production. The purpose of this study was to investigate the in vitro inflammatory action of HT in extracts of four OO varieties in the Languedoc region of the French Mediterranean. Factors other than cultivar were eliminated, which enabled unambiguous varietal differences to be identified. Purified extracts of OO were obtained using an optimized solid-phase extraction procedure by which only polar compounds were recovered. High performance liquid chromatography-photodiode array detection-tandem mass spectrometry was used to identify and quantify HT and oleacein in the extracts. The total polyphenol concentration ranged from 93.00 mg gallic acid equivalent/kg OO for Picholine to 27 mg gallic acid equivalent for Verdale OOs. The concentrations of HT in Picholine, Olivère, and Lucques varieties were 25.3, 18.8 and 12.1 mg/kg, respectively, whereas the concentration of HT in Verdale OOs was less, 1 mg/kg. The in vitro anti-inflammatory response of purified OO extracts, evaluated by the inhibition of nitric oxide release in lipopolysaccharide-induced interferon-γ activated J774.A1 macrophages, strongly correlated with total polyphenol content (R2 > 0.995). The effect increased asymptotically between the equivalent of 2 and 37 mg of OO, reaching, at the maximum tested concentration, 90%, 75%, 62%, and 30% activity for Picholine, Olivière, Lucques, and Verdale, respectively. The results presented here clearly show that, by comparison with authentic standards, the activity of HT in OO extracts was enhanced in a concentration-dependent manner, varying from 3-fold at the highest extract concentration to over 6.5-fold at the lowest extract concentration. Therefore, the anti-inflammatory activity of OOs should be rationalized on the basis of whole extracts rather than solely on the concentration of HT or other bioactive compounds in OO.

Molecular Analysis of the Official Algerian Olive Collection Highlighted a Hotspot of Biodiversity in the Central Mediterranean Basin.

Genetic diversity and population structure studies of local olive germplasm are important to safeguard biodiversity, for genetic resources management and to improve the knowledge on the distribution and evolution patterns of this species. In the present study Algerian olive germplasm was characterized using 16 nuclear (nuSSR) and six chloroplast (cpSSR) microsatellites. Algerian varieties, collected from the National Olive Germplasm Repository (ITAFV), 10 of which had never been genotyped before, were analyzed. Our results highlighted the presence of an exclusive genetic core represented by 13 cultivars located in a mountainous area in the North-East of Algeria, named Little Kabylie. Comparison with published datasets, representative of the Mediterranean genetic background, revealed that the most Algerian varieties showed affinity with Central and Eastern Mediterranean cultivars. Interestingly, cpSSR phylogenetic analysis supported results from nuSSRs, highlighting similarities between Algerian germplasm and wild olives from Greece, Italy, Spain and Morocco. This study sheds light on the genetic relationship of Algerian and Mediterranean olive germplasm suggesting possible events of secondary domestication and/or crossing and hybridization across the Mediterranean area. Our findings revealed a distinctive genetic background for cultivars from Little Kabylie and support the increasing awareness that North Africa represents a hotspot of diversity for crop varieties and crop wild relative species.

Linking belowground microbial network changes to different tolerance level towards Verticillium wilt of olive.

BACKGROUND: Verticillium wilt of olive (VWO) is caused by the soilborne fungal pathogen Verticillium dahliae. One of the best VWO management measures is the use of tolerant/resistant olive cultivars. Knowledge on the olive-associated microbiome and its potential relationship with tolerance to biotic constraints is almost null. The aims of this work are (1) to describe the structure, functionality, and co-occurrence interactions of the belowground (root endosphere and rhizosphere) microbial communities of two olive cultivars qualified as tolerant (Frantoio) and susceptible (Picual) to VWO, and (2) to assess whether these communities contribute to their differential disease susceptibility level. RESULTS: Minor differences in alpha and beta diversities of root-associated microbiota were detected between olive cultivars regardless of whether they were inoculated or not with the defoliating pathotype of V. dahliae. Nevertheless, significant differences were found in taxonomic composition of non-inoculated plants' communities, "Frantoio" showing a higher abundance of beneficial genera in contrast to "Picual" that exhibited major abundance of potential deleterious genera. Upon inoculation with V. dahliae, significant changes at taxonomic level were found mostly in Picual plants. Relevant topological alterations were observed in microbial communities' co-occurrence interactions after inoculation, both at structural and functional level, and in the positive/negative edges ratio. In the root endosphere, Frantoio communities switched to highly connected and low modularized networks, while Picual communities showed a sharply different behavior. In the rhizosphere, V. dahliae only irrupted in the microbial networks of Picual plants. CONCLUSIONS: The belowground microbial communities of the two olive cultivars are very similar and pathogen introduction did not provoke significant alterations in their structure and functionality. However, notable differences were found in their networks in response to the inoculation. This phenomenon was more evident in the root endosphere communities. Thus, a correlation between modifications in the microbial networks of this microhabitat and susceptibility/tolerance to a soilborne pathogen was found. Moreover, V. dahliae irruption in the Picual microbial networks suggests a stronger impact on the belowground microbial communities of this cultivar upon inoculation. Our results suggest that changes in the co-occurrence interactions may explain, at least partially, the differential VWO susceptibility of the tested olive cultivars. Video abstract.

Analysis of Microsatellites (SSRs) in Processed Olives as a Means of Cultivar Traceability and Authentication.

Select cultivars of table olives have more desirable traits and a higher economic value. There are suspected issues with cultivar mislabeling and traceability in the supply chain. Here, we describe a method to identify cultivars by genotyping of processed olives. DNA was extracted from leaves and California-style olives of seven commonly packed cultivars. Processed olive fruits yielded relatively low DNA concentrations (0.04-0.86 µg/g), and extracts had more impurities compared with leaves. From 15 candidate SSRs, five markers showing the highest number of unique allele combinations and discriminatory power were selected. These SSRs were successfully amplified and analyzed in all cultivars of olives except one. When directly comparing any two cultivars, different allele combinations were typically present for at least four of the five SSRs. Microsatellite analysis shows potential as a simple yet robust diagnostic tool. The method can be expanded to include other cultivars, styles of table olives, and potentially other processed plant-based foods.

Fresh and Aromatic Virgin Olive Oil Obtained from Arbequina, Koroneiki, and Arbosana Cultivars.

Three factors for the extraction of extra virgin olive oil (EVOO) were evaluated: diameter of the grid holes of the hammer-crusher, malaxation temperature, and malaxation time. A Box-Behnken design was used to obtain a total of 289 olive oil samples. Twelve responses were analyzed and 204 mathematical models were obtained. Olives from super-intensive rainfed or irrigated crops of the Arbequina, Koroneiki, and Arbosana cultivars at different stages of ripening were used. Malaxation temperature was found to be the factor with the most influence on the total content of lipoxygenase pathway volatile compounds; as the temperature increased, the content of volatile compounds decreased. On the contrary, pigments increased when the malaxation temperature was increased. EVOO from irrigated crops and from the Arbequina cultivar had the highest content of volatile compounds. Olive samples with a lower ripening degree, from the Koroneiki cultivar and from rainfed crops, had the highest content of pigments.

Characterization of Worldwide Olive Germplasm Banks of Marrakech (Morocco) and Córdoba (Spain): Towards management and use of olive germplasm in breeding programs.

Olive (Olea europaea L.) is a major fruit crop in the Mediterranean Basin. Ex-situ olive management is essential to ensure optimal use of genetic resources in breeding programs. The Worldwide Olive Germplasm Bank of Córdoba (WOGBC), Spain, and Marrakech (WOGBM), Morocco, are currently the largest existing olive germplasm collections. Characterization, identification, comparison and authentication of all accessions in both collections could thus provide useful information for managing olive germplasm for its preservation, exchange within the scientific community and use in breeding programs. Here we applied 20 microsatellite markers (SSR) and 11 endocarp morphological traits to discriminate and authenticate 1091 olive accessions belonging to WOGBM and WOGBC (554 and 537, respectively). Of all the analyzed accessions, 672 distinct SSR profiles considered as unique genotypes were identified, but only 130 were present in both collections. Combining SSR markers and endocarp traits led to the identification of 535 cultivars (126 in common) and 120 authenticated cultivars. No significant differences were observed between collections regarding the allelic richness and diversity index. We concluded that the genetic diversity level was stable despite marked contrasts in varietal composition between collections, which could be explained by their different collection establishment conditions. This highlights the extent of cultivar variability within WOGBs. Moreover, we detected 192 mislabeling errors, 72 of which were found in WOGBM. A total of 228 genotypes as molecular variants of 74 cultivars, 79 synonyms and 39 homonyms as new cases were identified. Both collections were combined to define the nested core collections of 55, 121 and 150 sample sizes proposed for further studies. This study was a preliminary step towards managing and mining the genetic diversity in both collections while developing collaborations between olive research teams to conduct association mapping studies by exchanging and phenotyping accessions in contrasted environmental sites.

Evolutionary transcriptomics reveals the origins of olives and the genomic changes associated with their domestication.

The olive (Olea europaea L. subsp. europaea) is one of the oldest and most socio-economically important cultivated perennial crop in the Mediterranean region. Yet, its origins are still under debate and the genetic bases of the phenotypic changes associated with its domestication are unknown. We generated RNA-sequencing data for 68 wild and cultivated olive trees to study the genetic diversity and structure both at the transcription and sequence levels. To localize putative genes or expression pathways targeted by artificial selection during domestication, we employed a two-step approach in which we identified differentially expressed genes and screened the transcriptome for signatures of selection. Our analyses support a major domestication event in the eastern part of the Mediterranean basin followed by dispersion towards the West and subsequent admixture with western wild olives. While we found large changes in gene expression when comparing cultivated and wild olives, we found no major signature of selection on coding variants and weak signals primarily affected transcription factors. Our results indicated that the domestication of olives resulted in only moderate genomic consequences and that the domestication syndrome is mainly related to changes in gene expression, consistent with its evolutionary history and life history traits.

Volatolomics approach by HS-SPME-GC-MS and multivariate analysis to discriminate olive tree varieties infected by Xylella fastidiosa.

INTRODUCTION: Xylella fastidiosa (Xf) is a pathogenic bacterium that causes diseases in olive trees. Therefore, analytical methods for both the characterisation of the host/pathogen interaction and infection monitoring are needed. Volatile organic compounds (VOCs) are emitted by plants relate to their physiological state, therefore VOCs monitoring can assist in detecting stress or infection states before visible signs are present. OBJECTIVE: In this work, the headspace-solid phase microextraction-gaschromatography-mass spectrometry (HS-SPME-GC-MS) technique was used for the first time to highlight VOCs differences between healthy and Xf-infected olive trees. METHODOLOGY: VOCs from olive tree twig samples were extracted and analysed by HS-SPME-GC-MS, and hence identified by comparing the experimental linear retention indexes with the reference values and by MS data obtained from NIST library. Data were processed by principal component analysis (PCA) and analysis of variance (ANOVA). RESULTS: The HS-SPME step was optimised in terms of adsorbent phase and extraction time. HS-SPME-GC-MS technique was applied to the extraction and analysis of VOCs of healthy and Xf-infected olive trees. More than 100 compounds were identified and the differences between samples were evidenced by the multivariate analysis approach. The results showed the marked presence of methyl esters in Xf-infected samples, suggesting their probable involvement in the mechanism of diffusible signal factor. CONCLUSION: The proposed approach represents an easy and solvent-free method to evaluate the presence of Xf in olive trees, and to evidence volatiles produced by host/pathogen interactions that could be involved in the defensive mechanism of the olive tree and/or in the infective action of Xf.

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

Species trees have traditionally been inferred from a few selected markers, and genome-wide investigations remain largely restricted to model organisms or small groups of species for which sampling of fresh material is available, leaving out most of the existing and historical species diversity. The genomes of an increasing number of species, including specimens extracted from natural history collections, are being sequenced at low depth. While these data sets are widely used to analyse organelle genomes, the nuclear fraction is generally ignored. Here we evaluate different reference-based methods to infer phylogenies of large taxonomic groups from such data sets. Using the example of the Oleeae tribe, a worldwide-distributed group, we build phylogenies based on single nucleotide polymorphisms (SNPs) obtained using two reference genomes (the olive and ash trees). The inferred phylogenies are overall congruent, yet present differences that might reflect the effect of distance to the reference on the amount of missing data. To limit this issue, genome complexity was reduced by using pairs of orthologous coding sequences as the reference, thus allowing us to combine SNPs obtained using two distinct references. Concatenated and coalescence trees based on these combined SNPs suggest events of incomplete lineage sorting and/or hybridization during the diversification of this large phylogenetic group. Our results show that genome-wide phylogenetic trees can be inferred from low-depth sequence data sets for eukaryote groups with complex genomes, and histories of reticulate evolution. This opens new avenues for large-scale phylogenomics and biogeographical analyses covering both the extant and the historical diversity stored in museum collections.

The Effect of Olive Varieties on Fatty Acid Composition and Tocopherol Contents of Cold Pressed Virgin Olive Oils.

In this study, fatty acid composition and tocopherol contents of cold pressed olive oils belonged to Ayvalik, Gemlik, Domat, Çilli, Çöpasi and Söbüasi varieties were determined. The fatty acid composition of the olive oils showed differences depending on the olive variety. The major fatty acids such as oleic, linoleic and palmitic acids were found as 62.49-68.53%; 8.30-17.93%; 14.39-19.47%, respectively. The highest oleic, linoleic and palmitic acid contents were determined in the varieties of Çilli (68.53%), Söbüasi (17.93%) and Gemlik (19.47%), respectively. Palmitic, oleic and linoleic fatty acids of the local varieties such as Çilli, Çöpasi, Söbüasi were similar to those of Ayvalik and Gemlik varieties. The most abundant isomer of tocopherol in olive oils was α-tocopherol (18.22-36.02 mg/100g). The highest α- and γ- tocopherols were observed in olive oils of Söbüasi variety (36.02 mg/100g) and Gemlik variety (8.12 mg/100g), respectively. It is concluded that the olive variety is an important factor on the fatty acid composition and tocopherol content of the olive oil.