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opencc-zeroDec 2012View details →

Data from: Genetic relationships, structure and parentage simulation among the olive tree (Olea europaea L. subsp. europaea) cultivated in Southern Italy revealed by SSR markers

In this work, we assess both the morphological and genetic diversity of 68 important olive cultivars from three Southern Italian regions: Calabria, Campania and Sicily. Twenty-five phenotypic traits were evaluated and 12 simple sequence repeat (SSR) markers were analysed. All SSR primers were polymorphic and reliable. The total number of alleles per locus varied from 5 to 19 with an average number of 13.1 and a mean polymorphic information content (PIC) of 0.81. These results suggested high genetic diversity within these three olive germplasm collections. Morphological traits also showed significant variability amongst cultivars. Two cases of identity were found and ten statistically significant cases of putative parent/sibling were discovered by performing a SSR-based parentage simulation analysis with CERVUS. The Mantel test indicated low but significant correlations between the morphological data and SSR allelic frequency, origin and SSR allelic frequency, and origin and morphology. Structure software allowed inference of relationships between the three olive germplasm collections and allowed us to obtain the most consistent grouping and to identify putative admixed or exchanged cultivars. Cluster and multivariate analysis, based on morphological traits, revealed geographic grouping in agreement with UPGMA dendrogram and structure analysis using SSRs. Sicilian cultivars showed a more homogenous genetic makeup, probably due to geographical isolation, whilst Calabrian and Campanian cultivars seemed to have a less distinct genetic structure, with a greater degree of intermixing. A correlation between the presence of certain SSR alleles and fruit size was also found.

opencc-zeroDec 2009View details →

Data from: The relevance of gene flow in metapopulation dynamics of an oceanic island endemic, Olea europaea subsp guanchica

Theoretical and empirical studies suggest that geographical isolation and extinction-recolonization dynamics are two factors causing strong genetic structure in metapopulations. Here, we investigated the effect of population age structure and isolation by distance in the patterns of genetic diversity in a tree species (Olea europaea subsp. guanchica) sporadically affected by volcanic events across the Canarian archipelago. Genetic variation was assessed at six nuclear microsatellites (nDNA) and six chloroplast fragments (cpDNA) in nine subpopulations sampled on four oceanic islands. Subpopulations occurring on more recent substrates were more differentiated than those on older substrates, but within-subpopulation genetic diversity was not significantly different between age groups for any type of marker. Contrary to the general trend for island systems, between-island differentiation was extremely low, and lower than differentiation between subpopulations on the same island. The pollen-to-seed ratio was close to one, two orders of magnitude lower than the average estimated for other wind-pollinated, animal-dispersed plants. Our results showed that population turnover and geographical isolation increased genetic differentiation relative to an island model at equilibrium, but overall genetic structure was unexpectedly weak for a species distributed among islands. This empirical study shows that extensive gene flow, particularly mediated by seeds, can ameliorate population subdivision resulting from extinction-recolonization dynamics and isolation by distance

opencc-zeroFeb 2022View details →

Genome assembly of Olea europaea subsp. cuspidate

Background: The Olive complex, comprised of six subspecies, are very valuable plants for global trade, human health, and food safety. However, only one subspecies (Olea europaea subsp. europaea, OE) and its wild form (Olea europaea subsp. europaea var. sylvestris, OS) have genomic references, hindering our understanding on the evolution of this species. Results: By utilizing a hybrid approach to incorporate Illumina, Nanopore, and Hi-C technology, we obtained by far the best reference genome assembly among wild olive subspecies for African olive, Olea europaea subsp cuspidate (OC) with contig and scaffold N50 values 3.83 Mb and 38.04 Mb, respectively. The assessment of protein-coding gene completeness revealed the high integrity of OC, which is at the similar level as OE assembly reported previously and much higher than that of OS. The divergence time between OC and the last common ancestor of OE and OS was estimated to be 4.21 Mya (95% CI: 1.43 - 7.31 Mya). The pathways of positively selected genes of OC are related to metabolism of cofactors and vitamins, indicating the potential medical and economic values of OC for further utilizing and research. The gene origination analyses revealed a substantial outburst (19.5%) of gene transposition events in the common ancestor of olive subspecies, suggesting the importance of olive speciation in shaping the new gene evolution of OC subspecies. Conclusions: In this study, we constructed the de novo assembly and protein-coding gene pool for Olea europaea subsp cuspidate (OC), which may facilitate the medical and breeding utilizations of this widely distributed olive close relative.

opencc-by-4.0Sep 2024View details →

Información suplementaria TFM "Determinación de los genes posiblemente relacionados con el estrés salino en Olea europaea

Material complementario del TFM “Determinación de los genes posiblemente relacionados con el estrés salino en Olea europaea” ·         in_comp_01.odf: tabla de datos en formato ODS con cuatro hojas que incluyen:. o   Hoja 1: Lista de genes de arabidopsis con el ortólogo correspondiente de acebuche. o   Hoja 2: Lista de genes de arabidopsis con el ortólogo correspondiente de “Farga” o   Hoja 3: Lista de genes de arabidopsis con el ortólogo correspondiente de “Arbquina” o   Hoja 4: Lista de genes de arabidopsis con el ortólogo correspondiente de “Picual” ·         in_comp_02.odf.: tabla de datos en formato ODS con dos hojas que incluyen:. o   Hoja 1: Lista con el recuento de genes enriquecidos en los procesos biológicas de arabidopsis, acebuche,  “Arbequina”, “Picual” y “Farga”. o   Hoja 1: Lista con el recuento de genes enriquecidos en las funciones moleculares de arabidopsis, acebuche, “Arbequina”, “Picual” y “Farga”. ·         in_comp_03.odf : tabla de datos en formato ODS con tres hojas que incluye: o   Hoja 1: Lista de los factores de transcripción de “Farga”. o   Hoja 2: Lista de los factores de transcripción de “Arbequina”. o   Hoja 3: Lista de los factores de transcripción de “Picual”.   ·         in_comp_04.odf : tabla de datos en formato ODS con cuatro hojas que incluye: o   Hoja 1: Recuento de factores de transcripción por familias de arabidopsis, acebuche, “Arbequina”, “Picual” y “Farga”. o   Hoja 2 : Proporción de factores de transcripción por familias respecto al total del organismo de arabidopsis, acebuche, “Arbequina”, “Picual” y “Farga”. ·         in_comp_05.odf: tabla de datos en formato ODS con tres hojas que incluye: o   Hoja 1: Lista de los factores de transcripción relacionados con el estrés salino de “Farga”. o   Hoja 2: Lista de los factores de transcripción relacionados con el estrés salino  de “Arbequina”. o   Hoja 3: Lista de los factores de transcripción relacionados con el estrés salino de “Picual”. ·         in_comp_06.odf: tabla de datos en formato ODS con cuatro hojas que incluyen:. o   Hoja 1: Lista de genes seleccionados de la bibliografía de arabidopsis con el ortólogo correspondiente de acebuche. o   Hoja 2: Lista de genes seleccionados de la bibliografía de arabidopsis con el ortólogo correspondiente de “Farga” o   Hoja 3: Lista de genes seleccionados de la bibliografía de arabidopsis con el ortólogo correspondiente de “Arbquina” o   Hoja 4: Lista de genes seleccionados de la bibliografía de arabidopsis con el ortólogo correspondiente de “Picual” ·         inf_comp_07.odf: in_comp_02.odf.: tabla de datos en formato ODS con dos hojas que incluyen:. o   Hoja 1: Recuento de genes seleccionados de la bibliografía enriquecidos en los procesos biológicas de arabidopsis, acebuche,  “Arbequina”, “Picual” y “Farga”. o   Hoja 1: Recuento de genes seleccionados de la bibliografía enriquecidos en las funciones moleculares de arabidopsis, acebuche, “Arbequina”, “Picual” y “Farga”.

Fig. 7 in Phenolic and lipophilic metabolite adjustments in Olea europaea (olive) trees during drought stress and recovery

Fig. 7. General overview of phenolic and lipophilic profile variation after stress treatments (exposure) and stress relief (recovery). Relative levels [expressed as log2 (stress/control)] are given besides each identified metabolite as a heatmap: WD – water deficit and WDHS+UVB – water deficit with heat and high UVB shocks. Nd - not detected.

Fig. 6 in Phenolic and lipophilic metabolite adjustments in Olea europaea (olive) trees during drought stress and recovery

Fig. 6. Carbohydrates profile of O. europaea leaves from plants under control (C) conditions and exposed to WD and WD HS+UVB treatments. Values are means ± standard deviation (n = 4). For each compound, the different letters indicate statistical between treatments (P <0.05).

Fig. 3 in Phenolic and lipophilic metabolite adjustments in Olea europaea (olive) trees during drought stress and recovery

Fig. 3. Fatty acids and sterols profiles of O. europaea leaves from plants under control (C) conditions and exposed to WD and WDHS+UVB treatments. Values are means ± standard deviation (n = 4). For each compound, the different letters indicate statistical between treatments (P <0.05).

Fig. 5 in Phenolic and lipophilic metabolite adjustments in Olea europaea (olive) trees during drought stress and recovery

Fig. 5. Terpenes profile of O. europaea leaves from plants under control (C) conditions and exposed to WD and WDHS+UVB treatments. Values are means ± standard deviation (n = 4). For each compound, the different letters indicate statistical between treatments (P <0.05).

Fig. 2 in Phenolic and lipophilic metabolite adjustments in Olea europaea (olive) trees during drought stress and recovery

Fig. 2. Secoiridoids and HCAds profiles of O. europaea leaves from plants under control (C) conditions and exposed to WD and WDHS+UVB treatments. Values are means ± standard deviation (n = 4). For each compound, the different letters indicate statistical between treatments (P <0.05). Nd – not detected (2′′- methoxyoleuropein was not detected in DS plants and methyloleuropein was not detected in DSHS+UVB plants during the stress recovery phase).

Fig. 1 in Phenolic and lipophilic metabolite adjustments in Olea europaea (olive) trees during drought stress and recovery

Fig. 1. Flavonoids profile of O. europaea leaves from plants under control conditions (C) and exposed to WD and WDHS+UVB treatments. Values are means ± standard deviation (n = 4). For each compound, the different letters indicate statistical differences between treatments (P <0.05).

Fig. 2. A in The antioxidant system in Olea europaea to enhanced UV-B radiation also depends on flavonoids and secoiridoids

Fig. 2. A - Variation in reduced (AsA) and oxidized ascorbate (DHA), B - AsA redox state (AsA/DHA), C - reduced (GSH) and oxidized glutathione (GSSG), and D - and glutathione redox potential (GSH/GSSG) in leaves of O. europaea plants under control conditions and exposed to UV-B treatments (UV–B1 and UV-B2). Values are mean ± s.d. (n = 6–8). For each parameter, different letters indicate statistical differences between treatments (P <0.05) base on Holms Sidak Comparison Test.

Fig. 2 in The antioxidant system in Olea europaea to enhanced UV-B radiation also depends on flavonoids and secoiridoids

Fig. 2 presents the changes of AsA, DHA, GSH and GSSG, AsA/DHA and GSH/GSSG in O. europaea leaves after UV-B exposure. Compared with controls, plants exposed to UV-B1 had decreased levels of both AsA and DHA, which led to a maintenance of the AsA/DHA ratio (P> 0.05, Fig. 2A and B). Contrarily, GSH levels decreased while the GSSG increased significantly, decreasing the GSH/GSSG ratio (P <0.05, Fig. 2C and D). Plants exposed to UV-B2 showed an increase of DHA and, mostly, of AsA pools, which led to an increase of the AsA/DHA ratio (P <0.05, Fig. 2A and B). On other hand GSH levels also increased but GSSG was not influenced, which supported the increase of GSH/GSSG (P <0.05, Fig. 2C and D).

Fig. 3. A in The antioxidant system in Olea europaea to enhanced UV-B radiation also depends on flavonoids and secoiridoids

Fig. 3. A - secoiridoids, B - flavonoids, and C - hydroxycinnamic acid derivatives in leaves of O. europaea plants under control conditions and exposed to UV-B treatments (UV–B1 and UV-B2). Values are mean ± s.d. (n = 3). For each compound, different letters indicate statistical differences between treatments (P <0.05) base on Holms Sidak Comparison Test.

Fig. 4 in The antioxidant system in Olea europaea to enhanced UV-B radiation also depends on flavonoids and secoiridoids

Fig. 4. General overview of the metabolites and antioxidant enzymes changes in O. europaea plants under UV-B doses: moderate (UV–B1) and high (UV–B2). Relative levels [expressed as log2 (UV–B/control)] are given besides (two colored rectangles) each identified metabolite/compound or enzyme activity as a heat-map, and the upper colored rectangle refers to UV-B1 treatment while the lower one refer to the UV-B2 treatment. Protective responses in O. europaea involve the activation of both enzymatic and non-enzymatic antioxidant mechanisms to control ROS (namely H2O2) homeostasis, but the enzymatic and AsA/GSH pools are more required by higher UV doses, while polyphenols pathways are similarly solicited by both treatments. UV-B1 treatment increases SOD, CAT and GPox activities and GSSG content, reducing Gr and APX activities and the contents of AsA, DHA and GSH. UV-B2 treatment, besides SOD, CAT and GPox activation, also increases Gr activity and the contents of AsA, DHA and GSH. Flavonoids (4ʹ or 3ʹ-methoxy luteolin glucoside and 4ʹ-methoxy luteolin decrease), secoiridoids (oleuropein decrease and 2ʹʹ- methoxyoleuropein increase) and HCAds (β-hydroxyverbascoside increase) respond similarly to both UV-B doses, putatively acting as UV-B shields and/or ROS scavengers.

publicJul 2010View details →

Data from: The relevance of gene flow in metapopulation dynamics of an oceanic island endemic, Olea europaea subsp guanchica

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publicMar 2013View details →

Data from: Genetic relationships, structure and parentage simulation among the olive tree (Olea europaea L. subsp. europaea) cultivated in Southern Italy revealed by SSR markers

Open the record for dataset details and reuse information.