Complete chloroplast genome sequence of historical olive (Olea europaea subsp. europaea) cultivar Mehras, in Jordan.
Ontology highlight
ABSTRACT:
SUBMITTER: Haddad N
PROVIDER: S-EPMC7849479 | biostudies-literature |
REPOSITORIES: biostudies-literature
Similar Datasets
Project description: Not available
| S-EPMC10796119 | biostudies-literature
Project description: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 Aureobasidium pullulans 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.
| S-EPMC4922053 | biostudies-literature
Project description:Oleaster (Olea europaea L. subsp. europaea var. sylvestris) is the ancestor of cultivated olive (Olea europaea L. subsp. europaea var. europaea) and it is spread through the whole Mediterranean Basin, showing an overlapping distribution with cultivated olive trees. Climate change and new emerging diseases are expected to severely affect the cultivations of olive in the future. Oleaster presents a higher genetic variability compared to the cultivated olive and some wild trees were found adapted to particularly harsh conditions; therefore, the role of oleaster in the future of olive cultivation may be crucial. Despite the great potential, only recently the need to deeply characterize and adequately preserve the wild olive resources drew the attention of researchers. In this review, we summarized the most important morphological and genetic studies performed on oleaster trees collected in different countries of the Mediterranean Basin. Moreover, we reviewed the strategies introduced so far to preserve and manage the oleaster germplasm collections, giving a future perspective on their role in facing the future agricultural challenges posed by climatic changes and new emerging diseases.
| S-EPMC8877956 | biostudies-literature
Project description:In olive, the response to environmental conditions, such as light availability, is under genetic control and requires a combination of biochemical and physiological events. We investigated the effect of irradiance in fruit development in two Italian cultivars, Leccino and Frantoio. Morphological and cyto-histological analyses, as well as water and oil content determination, were carried out in fruits exposed to a different light regime (named as light and shade fruits). Results demonstrated that the influence of light availability on fruit development depends on the cultivar. In Leccino, the fresh and the dry weight, the percentage of dry matter, the kernel and fruit diameter, the mesocarp thickness and the mesocarp cell size were higher in the light exposed fruits than in the ones grown in the shade. In Frantoio, differences between light and shade fruits were observed only at 140 DAF (Days After Flowering) and only in the kernel and fruit diameter and in the dry and fresh weight, which were higher in the light exposed fruits. Leccino, therefore, showed a greater sensitivity to the light availability. This may be related to the observed delay in the endocarp lignification as compared to the Frantoio cultivar. In each cultivar, moreover, shade and light fruits did not show differences in the timing of cell differentiation. Finally, the investigation of oil storage carried out in cyto-histological studies demonstrated that differences in oil content between fruit subjected to different light regimes correlated with the number of oil containing cells, rather than the oil content per cell. A different behaviour was observed in the two cultivars: in Leccino, the mesocarp cell size was almost twice of Frantoio, while oil drops were only 30% larger; therefore, the percentage of cell volume occupied by the oil drops was lower in Leccino than in Frantoio. The chemical analysis confirmed this observation.
| S-EPMC6446062 | biostudies-literature
Project description:In the face of climate change, water deficit and increasing soil salinity pose an even greater challenge to olive cultivation in the Mediterranean basin. Due to its tolerance to abiotic stresses, wild olive (Olea europaea subsp. europaea var. sylvestris) presents a good candidate in breeding climate-resilient olive varieties. In this study, the early response of the native Croatian wild olive genotype (WOG) to salinity was evaluated and compared with that of well-known cultivars (cv.) Leccino and Koroneiki. Potted olive plants were exposed either to 150 mM NaCl or 300 mM mannitol for 3 weeks to distinguish between the osmotic and ionic components of salt stress. To determine the impact of the plant age on salinity, 1-, 2-, and 3-year-old WOG plants were used in the study. The growth parameters of both the cultivars and WOG of different ages decreased in response to the mannitol treatment. In contrast to cv. Leccino, the NaCl treatment did not significantly affect the growth of cv. Koroneiki or WOG of any age. The contents of Na+ and Cl- were considerably higher in the salt-treated WOG, regardless of age, compared with the cultivars. However, while both treatments significantly reduced the K+ content of cv. Koroneiki, that nutrient was not significantly affected in either cv. Leccino or WOG. Unlike the cultivars and older WOG, the NaCl treatment caused a significant decline of photosynthetic pigments in the 1-year-old WOG. The cultivars and WOG of different ages experienced a similar drop in the chlorophyll a content under the isotonic mannitol treatment. The absence of lipid peroxidation, modulation of superoxide dismutase, and guaiacol peroxidase activity were noted in all WOG ages under both stressors. These data suggest that WOG resilience to salinity is associated with its large leaf capacity for Na+ and Cl- accumulation, K+ retention, and its adaptable antioxidative mechanisms. The results are promising with regard to obtaining a new olive cultivar with better resilience to soil salinity.
| S-EPMC8437259 | biostudies-literature
Project description: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.
| S-EPMC7203204 | biostudies-literature
Project description:Self-incompatibility (SI) is the main mechanism that favors outcrossing in plants. By limiting compatible matings, SI interferes in fruit production and breeding of new cultivars. In the Oleeae tribe (Oleaceae), an unusual diallelic SI system (DSI) has been proposed for three distantly related species including the olive (Olea europaea), but empirical evidence has remained controversial for this latter. The olive domestication is a complex process with multiple origins. As a consequence, the mixing of S-alleles from two distinct taxa, the possible artificial selection of self-compatible mutants and the large phenological variation of blooming may constitute obstacles for deciphering SI in olive. Here, we investigate cross-genotype compatibilities in the Saharan wild olive (O. e. subsp. laperrinei). As this taxon was geographically isolated for thousands of years, SI should not be affected by human selection. A population of 37 mature individuals maintained in a collection was investigated. Several embryos per mother were genotyped with microsatellites in order to identify compatible fathers that contributed to fertilization. While the pollination was limited by distance inside the collection, our results strongly support the DSI hypothesis, and all individuals were assigned to two incompatibility groups (G1 and G2). No self-fertilization was observed in our conditions. In contrast, crosses between full or half siblings were frequent (ca. 45%), which is likely due to a nonrandom assortment of related trees in the collection. Finally, implications of our results for orchard management and the conservation of olive genetic resources are discussed.
| S-EPMC7042767 | biostudies-literature
Project description:A transcriptomics approach was used as a tool to unravel gene regulatory network underlying salinity response in a salt-tolerant olive cultivar (cv. Kalamon) by simulating as much as possible olive growing conditions in the field. A 135 day long salinity experiment was conducted using one year old trees exposed to NaCl stress for 90 days followed by 45 days of post-stress period. Total RNA was extracted from the root samples after 15, 45 and 90 days of NaCl-treated and un-treated olive trees as well as after 15 and 45 days of post-treatment period and used for microarray hybridizations using a loop design. Hierarchical clustering of differentially expressed transcripts revealed two major, distinct clusters. Despite the limited number of probe set, a transcriptional regulatory networks was constructed for the salt-tolerant cultivar.
2012-11-20 | GSE36196 | GEO
Project description:Verticillium wilt of olive (VWO) is caused by the vascular pathogen Verticillium dahliae. One of the best VWO management measures is the use of tolerant cultivars; however, our knowledge on VWO tolerance/resistance genetics is very limited. A transcriptomic analysis was conducted to (i) identify systemic defense responses induced/repressed in aerial tissues of the tolerant cultivar Frantoio upon root colonization by V. dahliae, and (ii) determine the expression pattern of selected defense genes in olive cultivars showing differential susceptibility to VWO. Two suppression subtractive hybridization cDNA libraries, enriched in up-regulated (FU) and down-regulated (FD) genes respectively, were generated from "Frantoio" aerial tissues. Results showed that broad systemic transcriptomic changes are taking place during V. dahliae-"Frantoio" interaction. A total of 585 FU and 381 FD unigenes were identified, many of them involved in defense response to (a)biotic stresses. Selected genes were then used to validate libraries and evaluate their temporal expression pattern in "Frantoio." Four defense genes were analyzed in cultivars Changlot Real (tolerant) and Picual (susceptible). An association between GRAS1 and DRR2 gene expression patterns and susceptibility to VWO was observed, suggesting that these transcripts could be further evaluated as markers of the tolerance level of olive cultivars to V. dahliae.
| S-EPMC4584997 | biostudies-literature
Project description:The calibration of a reliable phenological model for olive grown in areas characterized by great environmental heterogeneity, like Italy, where many varieties exist, is challenging and often suffers from a lack of observations, especially on budbreak. In this study, we used a database encompassing many phenological events from different olive varieties, years, and sites scattered all over Italy to identify the phases in which site-enlarged developmental rates can be well regressed against air temperature (Developmental Rate function, DR) by testing both linear and nonlinear functions. A K-fold cross-validation (KfCV) was carried out to evaluate the ability of DR functions to predict phenological development. The cross-validation showed that the phases ranging from budbreak (BBCH 01 and 07) to flowering (BBCH 61 and 65) and from the beginning of flowering (BBCH 51) to flowering can be simulated with high accuracy (r2 = 0.93-0.96; RMSE = 3.9-6.6 days) with no appreciable difference among linear and nonlinear functions. Thus, the resulting DRs represent a simple yet reliable tool for regional phenological simulations for these phases in Italy, paving the way for a reverse modeling approach aimed at reconstructing the budbreak dates. By contrast, and despite a large number of phases explored, no appreciable results were obtained on other phases, suggesting possible interplays of different drivers that need to be further investigated.
| S-EPMC8230019 | biostudies-literature