Alternative pathways for phosphatidylcholine synthesis in olive (Olea europaea L.) callus cultures.
Ontology highlight
ABSTRACT:
SUBMITTER: Williams M
PROVIDER: S-EPMC1137515 | biostudies-other | 1994 Dec
REPOSITORIES: biostudies-other
Similar Datasets
Project description:As a prelude to detailed flux control analysis of lipid synthesis in plants, we have examined the latter in tissue cultures from two important oil crops, olive (Olea europaea L.) and oil palm (Elaeis guineensis Jacq.). Temperature was used to manipulate the overall rate of lipid formation in order to characterize and validate the system to be used for analysis. With [1-14C]acetate as a precursor, an increase in temperature from 20 to 30 degrees C produced nearly a doubling of total lipid labelling. This increase in total lipids did not change the radioactivity in the intermediate acyl-(acyl carrier protein) or acyl-CoA pools, indicating that metabolism of these pools did not exert any significant constraint for overall synthesis. In contrast, there were some differences in the proportional labelling of fatty acids and of lipid classes at the two temperatures. The higher temperature caused a decrease in polyunsaturated fatty acid labelling and an increase in the proportion of triacylglycerol labelling in both calli. The intermediate diacylglycerol was increased in olive, but not in oil palm. Overall the data indicate the suitability of olive and oil-palm cultures for the study of lipid synthesis and indicate that de novo fatty acid synthesis may exert more flux control than complex lipid assembly. In olive, diacylglycerol acyltransferase may exert significant flux control when lipid synthesis is rapid.
| S-EPMC1222583 | biostudies-other
Project description:The 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).A 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 %.The 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: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: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
Project description:A comparative transcriptomics approach was used as a tool to unravel gene regulatory networks underlying salinity response in olive trees by simulating as much as possible olive growing conditions in the field. Specifically, we investigated the genotype-dependent differences in the transcriptome response of two olive cultivars, a salt tolerant and a salt sensitive. A 135 day long comparative 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 for each cultivar. Despite the limited number of probe set, transcriptional regulatory networks were constructed for the salt-tolerant and salt-sensitive cultivar. The comparison of the salt responsive transcriptional regulatory networks in olive with those reported for Arabidopsis suggests that a tree species might respond in a similar to Arabidopsis way at the transcriptome level under salinity stress.
2012-11-20 | GSE36197 | GEO
Project description:The olive tree (Olea europaea L.) was one of the first plant species in history to be domesticated. Throughout olive domestication, gene expression has undergone drastic changes that may affect tissue/organ-specific genes. This is an RNA-seq study of the transcriptomic activity of different tissues/organs from adult olive tree cv. "Picual" under field conditions. This analysis unveiled 53,456 genes with expression in at least one tissue, 32,030 of which were expressed in all organs and 19,575 were found to be potential housekeeping genes. In addition, the specific expression pattern in each plant part was studied. The flower was clearly the organ with the most exclusively expressed genes, 3529, many of which were involved in reproduction. Many of these organ-specific genes are generally involved in regulatory activities and have a nuclear protein localization, except for leaves, where there are also many genes with a plastid localization. This was also observed in stems to a lesser extent. Moreover, pathogen defense and immunity pathways were highly represented in roots. These data show a complex pattern of gene expression in different organs, and provide relevant data about housekeeping and organ-specific genes in cultivated olive.
| S-EPMC7291012 | biostudies-literature
Project description:In 2014, high-throughput sequencing of libraries of total DNA from olive trees allowed the identification of two geminivirus-like contigs. After conventional resequencing of the two genomic DNAs, their analysis revealed they belonged to the same viral entity, for which the provisional name of Olea europaea geminivirus (OEGV) was proposed. Although DNA-A showed a genome organization similar to that of New World begomoviruses, DNA-B had a peculiar ORF arrangement, consisting of a movement protein (MP) in the virion sense and a protein with unknown function on the complementary sense. Phylogenetic analysis performed either on full-length genome or on coat protein, replication associated protein (Rep), and MP sequences did not endorse the inclusion of this virus in any of the established genera in the family Geminiviridae. A survey of 55 plants revealed that the virus is widespread in Apulia (Italy) with 91% of the samples testing positive, although no correlation of OEGV with a disease or specific symptoms was encountered. Southern blot assay suggested that the virus is not integrated in the olive genome. The study of OEGV-derived siRNA obtained from small RNA libraries of leaves and fruits of three different cultivars, showed that the accumulation of the two genomic components is influenced by the plant genotype while virus-derived-siRNA profile is in line with other geminivirids reported in literature. Single-nucleotide polymorphism (SNP) analysis unveiled a low intra-specific variability.
| S-EPMC8000510 | 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. Five experimental time-points were analyzed: 15days stress, 45days stress, 90days stress, 15days post-stress and 45days post-stress. In each timepoint treated and untreated (control) samples were obtained. Dye swap hybridizations and 4 biological replicates were performed for each treatment/timepoint in a loop design experimental setup. Low-quality arrays were not included in the data analysis (36 arrays/samples submitted). Each sample included three spot replicates.
2012-11-20 | E-GEOD-36196 | biostudies-arrayexpress
Project description:This is an RNA-seq study of the transcriptomic activity of different tissues from adult olive tree cv. Picual on field conditions. This analysis unveiled 53,456 genes with expression in at least one tissue; 32,030 of them were expressed in all organs and 19,575 were found to be potential housekeeping genes. In addition, the specific expression pattern in each part of the plant was studied. The flower was clearly the organ with the highest number of exclusive expressed genes, 3,529, and many of them were involved in reproduction. On the contrary, the stem only showed 229 exclusive expressed genes. The gene ontology (GO) terms analysis of these genes in each organ highlighted some tissue-specific pathways. In general, many of these organ-specific genes are involved in regulatory activities and have nuclear protein localization, with the exception of the leave, where there are also many genes whose coded proteins have plastid localization; to a lesser extent, this was also observed in stems. On the other hand, the pathogen defense and immunity pathways are highly represented in the roots. These data show a complex pattern of gene expression in different organs.
2020-05-07 | GSE140648 | GEO
Project description:A comparative transcriptomics approach was used as a tool to unravel gene regulatory networks underlying salinity response in olive trees by simulating as much as possible olive growing conditions in the field. Specifically, we investigated the genotype-dependent differences in the transcriptome response of two olive cultivars, a salt tolerant and a salt sensitive. A 135 day long comparative 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 for each cultivar. Despite the limited number of probe set, transcriptional regulatory networks were constructed for the salt-tolerant and salt-sensitive cultivar. The comparison of the salt responsive transcriptional regulatory networks in olive with those reported for Arabidopsis suggests that a tree species might respond in a similar to Arabidopsis way at the transcriptome level under salinity stress. Five experimental time-points were analyzed: 15days stress, 45days stress, 90days stress, 15days post-stress and 45days post-stress. In each timepoint treated and untreated (control) samples were obtained. Dye swap hybridizations and 4 biological replicates were performed for each treatment/timepoint in a loop design experimental setup. Each sample included three spot replicates.
2012-11-20 | E-GEOD-36197 | biostudies-arrayexpress