Ontology highlight
ABSTRACT:
PROVIDER: PRJNA799755 | ENA |
REPOSITORIES: ENA
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Project description:The invasive marine mussel Mytilus galloprovincialis has displaced the native congener Mytilus trossulus from central and southern California, but the native species remains dominant at more northerly sites that have high levels of freshwater input. To determine the extent to which interspecific differences in physiological tolerance to low salinity might explain limits to the invasive species’ biogeography, we used an oligonucleotide microarray to compare the transcriptional responses of these two species to an acute decrease in salinity. Among 6,777 genes on the microarray, 117 genes showed significant changes that were similar between species, and 12 genes showed significant species-specific responses to salinity stress. Osmoregulation and cell cycle control were important aspects of the shared transcriptomic response to salinity stress, whereas the genes with species-specific expression patterns were involved in mRNA splicing, polyamine synthesis, exocytosis, translation, cell adhesion, and cell signaling. Forty-five genes that changed expression significantly during salinity stress also changed expression during heat stress, but the direction of change in expression was typically opposite for the two forms of stress. These results (i) provide insights into the role of changes in gene expression in establishing physiological tolerance to acute decreases in salinity, and (ii) indicate that transcriptomic differences between M. galloprovincialis and M. trossulus in response to salinity stress are subtle and involve only a minor fraction of the overall suite of gene regulatory responses.
2011-01-10 | GSE25111 | GEO
Project description:Low salinity is one of the main factors limiting the distribution and survival of marine species. As a euryhaline species, the Pacific oyster Crassostrea gigas can be tolerant to relative low salinity. Through Illumina sequencing, we generated two transcriptomes with samples taken from gills of oysters exposed to the low salinity seawater versus the optimal seawater. By RNAseq technology, we found 1665 up-regulation genes and 1815 down-regulation genes that may regulate osmotic stress in C. gigas. As blasted by GO annotation and KEGG pathway mapping, functional annotation of the genes recovered diverse biological functions and processes. The genes regulated significantly were dominated in cellular process and regulation of biological process, intracellular and cell, binding and protein binding according to GO annotation. The results highlight genes related to osmoregulation and signaling and interactions of osmotic stress response, anti-apoptotic reactions as well as immune response, cell adhesion and communication, cytosqueleton and cell cycle. The study aimed to compare the expression data of the two transcriptomes to provide some useful insights into signal transduction pathways in oysters and offer a number of candidate genes as potential markers of tolerance to hypoosmotic stress for oysters. In addition, the characterization of C. gigas transcriptome will facilitate research into biological processes underlying physiological adaptations to hypoosmotic shock for marine invertebrates. Twelve Pacific oysters were exposed in low salinity (8‰) seawater and in optimal salinity (25‰) seawater, respectively. Gills from six oysters in each condition were balanced mixed respectively. The transcriptomes of two samples were generated by deep sequencing, using Illumina HiSeq2000.
2012-12-15 | E-GEOD-38022 | biostudies-arrayexpress
Project description:Oilseed mustard, Brassica juncea, exhibits high levels of genetic variability for salinity tolerance. To obtain the global view of transcriptome and investigate the molecular basis of salinity tolerance in a salt-tolerant variety CS52 of B. juncea, we performed transcriptome sequencing of control and salt-stressed seedlings. De novo assembly of 184 million high-quality paired-end reads yielded 42,327 unique transcripts longer than 300 bp with RPKM ≥1. When compared with non-redundant proteins, we could annotate 67% unigenes obtained in our study. Based on the mapping to expressed sequence tags (ESTs), 52.6% unigenes are novel compared to EST data available for B. juncea and constituent genomes. Differential expression analysis revealed altered expression of 1469 unigenes in response to salinity stress. Of these, 587, mainly associated with ROS detoxification, sulfur assimilation and calcium signaling pathways, are up regulated. Notable of these is RSA1 (SHORT ROOT IN SALT MEDIUM 1) INTERACTING TRANSCRIPTION FACTOR 1 (RITF1) homolog up regulated by >100 folds in response to stress. RITF1, encoding a bHLH transcription factor, is a positive regulator of SOS1 and several key genes involved in scavenging of salt stress-induced reactive oxygen species (ROS). Further, we performed comparative expression profiling of key genes implicated in ion homeostasis and sequestration (SOS1, SOS2, SOS3, ENH1, NHX1), calcium sensing pathway (RITF1) and ROS detoxification in contrasting cultivars, B. juncea and B. nigra, for salinity tolerance. The results revealed higher transcript accumulation of most of these genes in B. juncea var. CS52 compared to salt-sensitive cultivar even under normal growth conditions. Together, these findings reveal key pathways and signaling components that contribute to salinity tolerance in B. juncea var. CS52. We report transcriptome sequencing of two-weeks-old seedlings of B. juncea var. CS52 under normal growth conditions (CTRL) and in response to salinity stress (SS) using Illumina paired-end sequencing
2015-02-28 | E-GEOD-66389 | biostudies-arrayexpress
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: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:Low salinity is one of the main factors limiting the distribution and survival of marine species. As a euryhaline species, the Pacific oyster Crassostrea gigas can be tolerant to relative low salinity. Through Illumina sequencing, we generated two transcriptomes with samples taken from gills of oysters exposed to the low salinity seawater versus the optimal seawater. By RNAseq technology, we found 1665 up-regulation genes and 1815 down-regulation genes that may regulate osmotic stress in C. gigas. As blasted by GO annotation and KEGG pathway mapping, functional annotation of the genes recovered diverse biological functions and processes. The genes regulated significantly were dominated in cellular process and regulation of biological process, intracellular and cell, binding and protein binding according to GO annotation. The results highlight genes related to osmoregulation and signaling and interactions of osmotic stress response, anti-apoptotic reactions as well as immune response, cell adhesion and communication, cytosqueleton and cell cycle. The study aimed to compare the expression data of the two transcriptomes to provide some useful insights into signal transduction pathways in oysters and offer a number of candidate genes as potential markers of tolerance to hypoosmotic stress for oysters. In addition, the characterization of C. gigas transcriptome will facilitate research into biological processes underlying physiological adaptations to hypoosmotic shock for marine invertebrates.
2012-12-15 | GSE38022 | GEO
Project description:The mechanisms of cellular and molecular adaptation of fungi to salinity have been commonly drawn from halotolerant strains, although some exceptions in basidiomycete fungi can be found. These studies have been conducted in settings where cells are subjected to stress, either hypo or hyperosmotic, which can be a confounding factor in describing physiological mechanisms related to salinity. Here, we have studied transcriptomic changes in Aspergillus sydowii, a halophilic species, when growing in three different salinity conditions (No salt, 0.5M and 2.0M NaCl). In this fungus salinity related responses occur under high salinity (2.0M NaCl) and not when cultured under optimal conditions (0.5M NaCl), suggesting that in this species, most of the mechanisms described for halophilic growth are a consequence of saline stress response and not an adaptation to saline conditions.
2019-12-31 | GSE139804 | GEO
Project description:Low salinity is one of the main factors limiting the distribution and survival of marine species. As estuarine species, Crassostrea hongkongensis can live in relative low salinity. Through Illumina sequencing, we generated two transcriptomes with samples taken from gills of oysters exposed to the low salinity seawater versus the optimal seawater. By RNAseq technology, we found 13550 up-regulation genes and 9914 down-regulation genes that may regulate osmotic stress in C. hongkongensis. As blasted by GO annotation and KEGG pathway mapping, functional annotation of the genes recovered diverse biological functions and processes. The genes regulated significantly were dominated in structural molecule activity, intracellular,cytoplasm protein metabolism, biosynthesis,cell and transcription regulator activity according to GO annotation. The study aimed to compare the expression data of the two transcriptomes to provide some useful insights into signal transduction pathways in oysters and offer a number of candidate genes as potential markers of tolerance to hypoosmotic stress for oysters. In addition, the characterization of C. hongkongensis transcriptome will facilitate research into biological processes underlying physiological adaptations to hypoosmotic shock for marine invertebrates. Twelve oysters were exposed in low salinity (8‰) seawater and in optimal salinity (25‰) seawater,respectively. Gills from six oysters in each condition were balanced mixed respectively. The transcriptomes of two samples were generated by deep sequencing, using Illumina HiSeq2000
2014-10-01 | E-GEOD-51157 | biostudies-arrayexpress
Project description:The invasive marine mussel Mytilus galloprovincialis has displaced the native congener Mytilus trossulus from central and southern California, but the native species remains dominant at more northerly sites that have high levels of freshwater input. To determine the extent to which interspecific differences in physiological tolerance to low salinity might explain limits to the invasive species’ biogeography, we used an oligonucleotide microarray to compare the transcriptional responses of these two species to an acute decrease in salinity. Among 6,777 genes on the microarray, 117 genes showed significant changes that were similar between species, and 12 genes showed significant species-specific responses to salinity stress. Osmoregulation and cell cycle control were important aspects of the shared transcriptomic response to salinity stress, whereas the genes with species-specific expression patterns were involved in mRNA splicing, polyamine synthesis, exocytosis, translation, cell adhesion, and cell signaling. Forty-five genes that changed expression significantly during salinity stress also changed expression during heat stress, but the direction of change in expression was typically opposite for the two forms of stress. These results (i) provide insights into the role of changes in gene expression in establishing physiological tolerance to acute decreases in salinity, and (ii) indicate that transcriptomic differences between M. galloprovincialis and M. trossulus in response to salinity stress are subtle and involve only a minor fraction of the overall suite of gene regulatory responses. Two species (Mytilus galloprovincialis, Mytilus trossulus), hypo-osmotic shock for four hours (850 mOs/kg), one control group (1000 mOs/kg) sampled at the end of the treatment exposure (850 mOs/kg), one control group (1000 mOs/kg) sampled at the beginning. Biological replicates: 6 in each treatment group, 6 in each control group. Heterologous and homologous hybridization to a microarray constructed from Mytilus californianus and Mytilus galloprovincialis sequences. A reference design that used separate pools of reference RNA for each species was employed. Reference amplified RNA (aRNA) was created for each species by pooling RNA before and after amplification. The reference pool was made up of RNA from six different samples: two base-line control samples from the beginning of the experiment, two treatment samples from the end of the four-hour hypo-osmotic exposure, and two time-control samples from the end of the four-hour exposure time. To accurately compare the transcriptomes of Mytilus galloprovincialis and M. trossulus, we chose to develop a common microarray format that could be used for both species. This microarray design consisted of probe sequences generated from the out-group species, M. californianus. M. trossulus and M. galloprovincialis are approximately 7.5 million years divergent from M. californianus, yet only 3.5 million years divergent from each other (Seed, 1992). Therefore, heterologous hybridization to the microarray allowed us to compare transcriptional responses of M. galloprovincialis and M. trossulus without the inherent sequence biases that would result from a microarray that was designed from sequences of either M. galloprovincialis or M. trossulus. A limited number of sequences (556) from ESTs from M. galloprovincialis that matched M. californianus ESTs were included on the microarray to test for the effects of sequence mismatches. Only probes that performed well for both M. galloprovincialis and M. trossulus were used in our analyses. In order to determine significant changes in expression, we conducted a two-way ANOVA, in which salinity and species were modeled as fixed effects, and focused on genes that were significant for the salinity effect or the species x temperature interaction. We ignored the species term from the ANOVA as this effect could have highlighted genes that differentially bound to probes on the microarray due to differences in sequence homology, thus not reflecting true differences in gene expression. In accordance with statistical convention, all genes with a significant species x temperature interaction were deemed not to have significant temperature effects, even if the temperature term from the ANOVA had a low P-value. All genes with FDR-corrected (Benjamini and Hochberg, 1995) P-values less than 0.05 were considered significant. Analyses were conducted in the R statistical programming environment (R Development Core Team, 2009).
2011-01-10 | E-GEOD-25111 | biostudies-arrayexpress
Project description:Low salinity is one of the main factors limiting the distribution and survival of marine species. As estuarine species, Crassostrea hongkongensis can live in relative low salinity. Through Illumina sequencing, we generated two transcriptomes with samples taken from gills of oysters exposed to the low salinity seawater versus the optimal seawater. By RNAseq technology, we found 13550 up-regulation genes and 9914 down-regulation genes that may regulate osmotic stress in C. hongkongensis. As blasted by GO annotation and KEGG pathway mapping, functional annotation of the genes recovered diverse biological functions and processes. The genes regulated significantly were dominated in structural molecule activity, intracellular,cytoplasm protein metabolism, biosynthesis,cell and transcription regulator activity according to GO annotation. The study aimed to compare the expression data of the two transcriptomes to provide some useful insights into signal transduction pathways in oysters and offer a number of candidate genes as potential markers of tolerance to hypoosmotic stress for oysters. In addition, the characterization of C. hongkongensis transcriptome will facilitate research into biological processes underlying physiological adaptations to hypoosmotic shock for marine invertebrates.
2014-10-01 | GSE51157 | GEO