Comparative transcriptome analysis of two olive (Olea europaea L.) cultivars in response to NaCl stress
Ontology highlight
ABSTRACT:
ORGANISM(S): Olea europaea
PROVIDER: GSE36198 | GEO | 2012/11/20
SECONDARY ACCESSION(S): PRJNA152867
REPOSITORIES: GEO
Similar Datasets
Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series
2012-11-20 | E-GEOD-36198 | biostudies-arrayexpress
Project description:BackgroundOlive (Olea europaea L.) cultivation is rapidly expanding and low quality saline water is often used for irrigation. The molecular basis of salt tolerance in olive, though, has not yet been investigated at a system level. In this study 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 one.Methodology/principal findingsA 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 during the summer. A cDNA library made of olive seedling mRNAs was sequenced and an olive microarray was constructed. Total RNA was extracted from root samples after 15, 45 and 90 days of NaCl-treatment as well as after 15 and 45 days of post-treatment period and used for microarray hybridizations. SAM analysis between the NaCl-stress and the post-stress time course resulted in the identification of 209 and 36 differentially expressed transcripts in the salt-tolerant and salt-sensitive cultivar, respectively. Hierarchical clustering revealed two major, distinct clusters for each cultivar. Despite the limited number of probe sets, transcriptional regulatory networks were constructed for both cultivars while several hierarchically-clustered interacting transcription factor regulators such as JERF and bZIP homologues were identified.Conclusions/significanceA systems biology approach was used and differentially expressed transcripts as well as regulatory interactions were identified. The comparison of the interactions among transcription factors in olive with those reported for Arabidopsis might indicate similarities in the response of a tree species with Arabidopsis at the transcriptional level under salinity stress.
| S-EPMC3431368 | 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:Olive (Olea europaea L.) is one of the most important crops in the Mediterranean region. The expansion of cultivation in areas irrigated with low quality and saline water has negative effects on growth and productivity however the investigation of the molecular basis of salt tolerance in olive trees has been only recently initiated. To this end, we investigated the molecular response of cultivar Kalamon to salinity stress using next-generation sequencing technology to explore the transcriptome profile of olive leaves and roots and identify differentially expressed genes that are related to salt tolerance response. Out of 291,958 obtained trimmed reads, 28,270 unique transcripts were identified of which 35% are annotated, a percentage that is comparable to similar reports on non-model plants. Among the 1,624 clusters in roots that comprise more than one read, 24 were differentially expressed comprising 9 down- and 15 up-regulated genes. Respectively, inleaves, among the 2,642 clusters, 70 were identified as differentially expressed, with 14 down- and 56 up-regulated genes. Using next-generation sequencing technology we were able to identify salt-response-related transcripts. Furthermore we provide an annotated transcriptome of olive as well as expression data, which are both significant tools for further molecular studies in olive.
| S-EPMC4648586 | 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. 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
Project description:Olive breeding programmes are focused on selecting for traits as short juvenile period, plant architecture suited for mechanical harvest, or oil characteristics, including fatty acid composition, phenolic, and volatile compounds to suit new markets. Understanding the molecular basis of these characteristics and improving the efficiency of such breeding programmes require the development of genomic information and tools. However, despite its economic relevance, genomic information on olive or closely related species is still scarce. We have applied Sanger and 454 pyrosequencing technologies to generate close to 2 million reads from 12 cDNA libraries obtained from the Picual, Arbequina, and Lechin de Sevilla cultivars and seedlings from a segregating progeny of a Picual × Arbequina cross. The libraries include fruit mesocarp and seeds at three relevant developmental stages, young stems and leaves, active juvenile and adult buds as well as dormant buds, and juvenile and adult roots. The reads were assembled by library or tissue and then assembled together into 81 020 unigenes with an average size of 496 bases. Here, we report their assembly and their functional annotation.
| S-EPMC3576661 | biostudies-literature
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:Eight accessions of olive trees from three common varieties in Palestine, Nabali Baladi, Nabali Mohassan and Surri, were genetically evaluated using five simple sequence repeat (SSR) markers. A total of 17 alleles from 5 loci were observed in which 15 (88.2%) were polymorphic and 2 (11.8%) were monomorphic. An average of 3.4 alleles per locus was found ranging from 2.0 alleles with the primers GAPU-103 and DCA-9 to 5.0 alleles with U9932 and DCA-16. The smallest amplicon size observed was 50 bp with the primer DCA-16, whereas the largest one (450 bp) with the primer U9932. Cluster analysis with the unweighted pair group method with arithmetic average (UPGMA) showed three clusters: a cluster with four accessions from the 'Nabali Baladi' cultivar, another cluster with three accessions that represents the 'Nabali Mohassen' cultivar and finally the 'Surri' cultivar. The similarity coefficient for the eight olive tree samples ranged from a maximum of 100% between two accessions from Nabali Baladi and also in two other samples from Nabali Mohassan, to a minimum similarity coefficient (0.315) between the Surri and two Nabali Baladi accessions. The results in this investigation clearly highlight the genetic dissimilarity between the three main olive cultivars that have been misidentified and mixed up in the past, based on conventional morphological characters.
| S-EPMC4433930 | biostudies-other
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:Plant reproductive transcriptomes have been analyzed in different species due to the agronomical and biotechnological importance of plant reproduction. Here we presented an olive tree reproductive transcriptome database with samples from pollen and pistil at different developmental stages, and leaf and root as control vegetative tissues http://reprolive.eez.csic.es). It was developed from 2,077,309 raw reads to 1,549 Sanger sequences. Using a pre-defined workflow based on open-source tools, sequences were pre-processed, assembled, mapped, and annotated with expression data, descriptions, GO terms, InterPro signatures, EC numbers, KEGG pathways, ORFs, and SSRs. Tentative transcripts (TTs) were also annotated with the corresponding orthologs in Arabidopsis thaliana from TAIR and RefSeq databases to enable Linked Data integration. It results in a reproductive transcriptome comprising 72,846 contigs with average length of 686 bp, of which 63,965 (87.8%) included at least one functional annotation, and 55,356 (75.9%) had an ortholog. A minimum of 23,568 different TTs was identified and 5,835 of them contain a complete ORF. The representative reproductive transcriptome can be reduced to 28,972 TTs for further gene expression studies. Partial transcriptomes from pollen, pistil, and vegetative tissues as control were also constructed. ReprOlive provides free access and download capability to these results. Retrieval mechanisms for sequences and transcript annotations are provided. Graphical localization of annotated enzymes into KEGG pathways is also possible. Finally, ReprOlive has included a semantic conceptualisation by means of a Resource Description Framework (RDF) allowing a Linked Data search for extracting the most updated information related to enzymes, interactions, allergens, structures, and reactive oxygen species.
| S-EPMC4531244 | biostudies-literature