Project description:The marine teleost intestine plays a vital role in whole body salt and water homeostasis. Marine fish must drink seawater in order to rehydrate, and processing of that seawater throughout the gastrointestinal tract allows for the extraction of water from this highly hyperosmotic source. Although the molecular mechanisms of this process have been the subject of much investigation, numerous questions remain. Here, Gulf toadfish (Opsanus beta) were acclimated to normal seawater (35 ppt) of hypersaline seawater (60 ppt) and changes in the anterior intestine, posterior intestine, and intestinal fluid proteomes were investigated using a shotgun proteomics approach employing isobaric TMT tags.
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
Project description:Environmental sex determination (ESD) occurs in divergent, phylogenetically unrelated taxa, and in some species co-occurs with genetic sex determination (GSD) mechanisms. Although epigenetic regulation in response to environmental effects has long been proposed to be associated with ESD, a systemic analysis on epigenetic regulation of ESD is still lacking. Using half-smooth tongue sole (Cynoglossus semilaevis) as a model – a marine fish which has both ZW chromosomal GSD and temperature-dependent ESD – we investigated the role of DNA methylation in transition from GSD to ESD by comparing gonadal DNA methylomes of parental females, parental pseudo-males, F1 females, F1 pseudo-males and normal males. To assess the gonadal DNA methylome patterns across different sexual types of tongue sole, we carried out BS-seq on bisulfite converted DNA extracted from adult gonads of parental females, parental pseudo-males, and F1 pseudo-males and females from a cross between a parental pseudo-male and a normal female. We also sampled normal male individuals as a control for the normal male DNA methylation pattern. For each of the five samples, two biological replicates were utilized, with each replicate being pooled by five fish. The phenotype and genotype of each selected fish was identified by the histological analysis and PCR validation using the W chromosome specific marker. DNA were isolated from five pooled gonads of the same replicate, then 5 μg DNA was used to do the bisulfite conversion and BS-seq. The bisulfite conversion of sample DNA was carried out using a modified NH4HSO3-based protocol (Hayatsu et al. 2006). The paired-end library construction and sequencing were carried out using Illumina HiSeq 2000, according to the manufacturer’s instructions (Illumina). We also mixed 25 ng cl857 Sam7 Lambda DNA in each sample to use as conversion quality control for each library.
Project description:Three-spined stickleback (Gasterosteus aculeatus) represents a convenient model to study microevolution - adaptation to freshwater environment. While genetic adaptations to freshwater are well-studied, epigenetic adaptations attracted little attention. In this work, we investigated the role of DNA methylation in the adaptation of marine stickleback population to freshwater conditions. DNA methylation profiling was performed in marine and freshwater populations of sticklebacks, as well as in marine sticklebacks placed into freshwater environment and freshwater sticklebacks placed into seawater. For the first time, we demonstrated that genes encoding ion channels kcnd3, cacna1fb, gja3 are differentially methylated between marine and freshwater populations. We also showed that after placing marine stickleback into fresh water, its DNA methylation profile partially converges to the one of a freshwater stickleback. This suggests that immediate epigenetic response to freshwater conditions can be maintained in freshwater population. Interestingly, we observed enhanced epigenetic plasticity in freshwater sticklebacks that may serve as a compensatory regulatory mechanism for the lack of genetic variation in the freshwater population. Some of the regions that were reported previously to be under selection in freshwater populations also show differential methylation. Thus, epigenetic changes might represent a parallel mechanism of adaptation along with genetic selection in freshwater environment. Overall design: The following sample groups were studied: 1) marine sticklebacks kept in marine water, their natural habitat (M@M); 2) freshwater sticklebacks kept in freshwater (F@F); 3) marine sticklebacks incubated in fresh water for 4 days (M@F); 4) freshwater sticklebacks incubated in marine water for 4 days (F@M). In each gruop, 3 individual fish were profiled.
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.
Project description:Feral organisms are affected by adverse environmental factors present in their habitat. It was hypothesized that transcript expression pattern in a suitable target organ of a sentinel feral organism compared to a reference transcript population may serve as a comprehensive biomarker of these adverse effects. This study was aimed at inquiring the applicability of such biomarker and establishing a procedure for its appropriate utilization. The examined system contains dual-labeled microarray-based evaluation of the hepatic transcript expression pattern in a sentinel fish sampled in two habitats, a polluted (Haifa Bay) and a clean (Dor) site, respectively, for two years. The hepatic expression patterns were compared to a reference RNA assumed to represent specimens that have no exposure history to pollution. The sentinel fish is Lithognathus mormyrus, which inhabits a marine coastal habitat along the Mediterranean coast of Israel. The hepatic transcript expression patterns were evaluated using a 1152-clone cDNA microarray, biased towards pollution-affected genes. The LIMMA software was used to calculate the log2 ratios of expressions (M) and to identify the differentially expressed genes in each sample (adjusted P<0.01). Keywords: Response of fish hepatic gene expression pattern to environmental conditions. Overall design: Fish were sampled at each of two sites each year. All fish were hybridized to a common reference RNA population using a dye swap design. Hence, each fish was hybridized twice vs the reference RNA. The hybridization results were reanalysed by LIMMA using new division to samples.
Project description:We investigated salinity adaptation during the migration from freshwater to seawater of European eel (Anguilla anguilla) by examining the hypothesis that: The brain is the central organ for the co-ordination of environmental cues (day length, photoperiod, temperature and environmental salinity) with the anatomical and physiological adaptations which accompany pre-migrational morphogenesis and the osmoregulatory plasticity seen in post-migrational, salinity-adapted fish. We have characertised the mRNA expression profiles for the brains of fresh water and sea water adapted silver eel using a highly representative brain cDNA microarray. The array comprises 5760 cDNA clones from A.anguilla ranging from 0.5 -10 kb and an estimated redundancy of > 5 %.
Project description:We report the application of Solexa/Illumina’s RNA-seq sequencing approaches for transcriptome in a marine fish under different conditions (bacterial- and mock-challenged conditions). By obtaining over four billion bases of sequence from the cDNA, we generated 169,950 none-redundant consensus sequences, from which 44842 functional transcripts with complete or various length of encoding regions were identified. More than 52% of these transcripts could be enriched in approximately 219 known metabolic or signaling pathways, among of which 2673 transcripts were found to be associated with immune-relevant genes. Besides, about 8% of the transcripts seemed fish-specific genes that have never been described before. This study provides a framework for the application of comprehensive chromatin profiling towards characterization of diverse mammalian cell populations. Our study provided a global survey of the gene activities in host defense against bacterial infection in a non-model marine fish. Examination of different transcriptome in baterial- and mock challenged fish.