Gene expression differences between fast and slow growing individuals of carpet-shell clam (Ruditapes decussatus) assessed with a microarray
Ontology highlight
ABSTRACT:
ORGANISM(S): Ruditapes decussatus
PROVIDER: GSE99244 | GEO | 2017/05/25
SECONDARY ACCESSION(S): PRJNA387682
REPOSITORIES: GEO
Similar Datasets
Project description:Gene expression profiles of fast and slow growing adult individuals of Ruditapes decussatus
2017-05-25 | GSE99243 | GEO
Project description:Gene expression profiles of fast and slow growing adult individuals of Ruditapes decussatus
2017-05-25 | GSE99242 | GEO
Project description:Gene expression differences between fast and slow growing individuals of carpet-shell clam (Ruditapes decussatus) assessed with a microarray
| PRJNA387682 | ENA
Project description:Growth rate is one of the most important traits from the point of view of individual fitness and commercial production in mollusks, but its molecular and physiological basis is poorly known. We have studied differential gene expression related to differences in growth rate in adult individuals of the commercial marine clam Ruditapes decussatus. Gene expression in the gills and the digestive gland was analyzed in 5 fast-growing and five slow-growing animals by means of an oligonucleotide microarray containing 14,003 probes. A total of 356 differentially expressed genes (DEG) were found. We tested the hypothesis that differential expression might be concentrated at the growth control gene core (GCGC), i.e., the set of genes that underlie the molecular mechanisms of genetic control of tissue and organ growth and body size, as demonstrated in model organisms. The GCGC includes the genes coding for enzymes of the insulin/insulin-like growth factor signaling pathway (IIS), enzymes of four additional signaling pathways (Raf/Ras/Mapk, Jnk, TOR, and Hippo), and transcription factors acting at the end of those pathways. Only two out of 97 GCGC genes present in the microarray showed differential expression, indicating a very little contribution of GCGC genes to growth-related differential gene expression. Forty eight DEGs were shared by both organs, with gene ontology (GO) annotations corresponding to transcription regulation, RNA splicing, sugar metabolism, protein catabolism, immunity, defense against pathogens, and fatty acid biosynthesis. GO term enrichment tests indicated that genes related to growth regulation, development and morphogenesis, extracellular matrix proteins, and proteolysis were overrepresented in the gills. In the digestive gland overrepresented GO terms referred to gene expression control through chromatin rearrangement, RAS-related small GTPases, glucolysis, and energy metabolism. These analyses suggest a relevant role of, among others, some genes related to the IIS, such as the ParaHox gene Xlox, CCAR and the CCN family of secreted proteins, in the regulation of growth in bivalves.
| S-EPMC5712350 | biostudies-literature
Project description:An R.decussatus microarray platform was developed to to profile gene expression in R. decussatus heavy infected by Perkinsus olseni
2012-08-01 | GSE36276 | GEO
Project description:BACKGROUND: The Grooved Carpet shell clam Ruditapes decussatus is the autochthonous European clam and the most appreciated from a gastronomic and economic point of view. The production is in decline due to several factors such as Perkinsiosis and habitat invasion and competition by the introduced exotic species, the manila clam Ruditapes philippinarum. After we sequenced R. decussatus transcriptome we have designed an oligo microarray capable of contributing to provide some clues on molecular response of the clam to Perkinsiosis. RESULTS: A database consisting of 41,119 unique transcripts was constructed, of which 12,479 (30.3%) were annotated by similarity. An oligo-DNA microarray platform was then designed and applied to profile gene expression in R. decussatus heavily infected by Perkinsus olseni. Functional annotation of differentially expressed genes between those two conditionswas performed by gene set enrichment analysis. As expected, microarrays unveil genes related with stress/infectious agents such as hydrolases, proteases and others. The extensive role of innate immune system was also analyzed and effect of parasitosis upon expression of important molecules such as lectins reviewed. CONCLUSIONS: This study represents a first attempt to characterize Ruditapes decussatus transcriptome, an important marine resource for the European aquaculture. The trancriptome sequencing and consequent annotation will increase the available tools and resources for this specie, introducing the possibility of high throughput experiments such as microarrays analysis. In this specific case microarray approach was used to unveil some important aspects of host-parasite interaction between the Carpet shell clam and Perkinsus, two non-model species, highlighting some genes associated with this interaction. Ample information was obtained to identify biological processes significantly enriched among differentially expressed genes in Perkinsus infected versus non-infected gills. An overview on the genes related with the immune system on R. decussatus transcriptome is also reported.
| S-EPMC4007648 | biostudies-literature
Project description:An R.decussatus microarray platform was developed to to profile gene expression in R. decussatus heavy infected by Perkinsus olseni A comparative analysis of gene expression was conducted between Grooved carpet shell clam R. decussatus individuals for non infected and infected by Perkinsus olseni clam gills. Gene expression profiling was performed using an R.decussatus oligo-DNA microarray of 43,758 probes based on single-colour detection (Cyanine-3 only). Microarrays were scanned with Agilent scanner G2565BA at a resolution of 5 microns; all slides were scanned twice at two different sensitivity settings (XDRHi 100% and XDRLo 10%); the scanner software created a unique ID for each pair of XDR scans and saved it to both scan image files. Feature Extraction (FE) 9.5 used XDR ID to link the pairs of scans together automatically when extracting data. The signal left after all the FE processing steps have been completed is ProcessedSignal that contains the Multiplicatively Detrended, Background-Subtracted Signal.
2012-07-31 | E-GEOD-36276 | biostudies-arrayexpress
Project description:Transcriptional profiling of populations in the clam Ruditapes decussatus determined differentiation in gene-expression along parallel temperature gradients and between races of the Atlantic Ocean and West Mediterranean sea.
2023-04-04 | GSE223000 | GEO
Project description:Despite the large number of animal complete mitochondrial genomes currently available in public databases, knowledge about mitochondrial genomics in invertebrates is uneven. This paper reports, for the first time, the complete mitochondrial genome of the grooved carpet shell, Ruditapes decussatus, also known as the European clam. Ruditapes decussatus is morphologically and ecologically similar to the Manila clam Ruditapes philippinarum, which has been recently introduced for aquaculture in the very same habitats of Ruditapes decussatus, and that is replacing the native species. Currently the production of the European clam is almost insignificant, nonetheless it is considered a high value product, and therefore it is an economically important species, especially in Portugal, Spain and Italy. In this work we: (i) assembled Ruditapes decussatus mitochondrial genome from RNA-Seq data, and validated it by Sanger sequencing; (ii) analyzed and characterized the Ruditapes decussatus mitochondrial genome, comparing its features with those of other venerid bivalves; (iii) assessed mitochondrial sequence polymorphism (SP) and copy number variation (CNV) of tandem repeats across 26 samples. Despite using high-throughput approaches we did not find evidence for the presence of two sex-linked mitochondrial genomes, typical of the doubly uniparental inheritance of mitochondria, a phenomenon known in ?100 bivalve species. According to our analyses, Ruditapes decussatus is more genetically similar to species of the Genus Paphia than to the congeneric Ruditapes philippinarum, a finding that bolsters the already-proposed need of a taxonomic revision. We also found a quite low genetic variability across the examined samples, with few SPs and little variability of the sequences flanking the control region (Largest Unassigned Regions (LURs). Strikingly, although we found low nucleotide variability along the entire mitochondrial genome, we observed high levels of length polymorphism in the LUR due to CNV of tandem repeats, and even a LUR length heteroplasmy in two samples. It is not clear if the lack of genetic variability in the mitochondrial genome of Ruditapes decussatus is a cause or an effect of the ongoing replacement of Ruditapes decussatus with the invasive Ruditapes philippinarum, and more analyses, especially on nuclear sequences, are required to assess this point.
| S-EPMC5571815 | biostudies-literature
Project description:Copper (Cu) is a ubiquitous trace element in the aquatic environment, and is usually found at low levels. Copper environmental concentrations can be altered as a result anthropogenic activities. Shellfish are useful bioindicators to ensure adequate environmental monitoring. Thus, the aim of the present study was as follows: (a) determine the LC50 of copper(I) chloride in grooved carpet shell (Ruditapes decussatus) collected in the Santa Gilla lagoon (Sardinia, Italy), and (b) analyze the antioxidant biomarkers in digestive gland and gills of same specimens exposed to different concentrations of the above-mentioned metal (0.045, 0.45, and 0.90 mg/L) for 96 h. A withdrawal period of 96 h was considered for the treated clam, carrying out the same biochemical analyses, superoxide dismutase (SOD), catalase (CAT), selenium-dependent glutathione peroxidase (Se-GPx), glutathione S-transferases (GSTs), and total glutathione (GSH+2GSSG) in the two tissues. Different time and dose responses of the antioxidant biomarkers were recorded in the digestive glands and gills. Oxidative stress biomarkers highlighted the ability of Cu to induce oxidative stress in R. decussatus. Clam, following the withdrawal period of 96 h, has not been able to achieve the control levels of all biochemical markers in the digestive gland and gills. R. decussatus can be a suitable model to assess the ecotoxicity of copper in aquatic ecosystems. These findings may advance knowledge on the role and the effects of copper on oxidative stress biomarkers in grooved carpet shell. The metal ecotoxicity response can be useful to perform accurate biomarker-based monitoring programs using this bivalve species.
| S-EPMC9686603 | biostudies-literature