Enchytraeus crypticus
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PROVIDER: PRJNA225581 | ENA |
REPOSITORIES: ENA
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Project description:The soil worm Enchytraeus crypticus (oligochaete) is an ecotoxicology model species although without genome or transcriptome sequence information. The present research aimed at studying, via high-throughput pyrosequencing, the transcriptome of Enchytraeus crypticus, sampled from multiple test conditions, and the construction of a high-density microarray for functional genomic studies. A pyrosequencing run retrieved approximately 1.5 million reads representing 645 million bases. After assembly, 27,296 contigs and 87,686 singletons were obtained. from which 44% and 25% were annotated as protein-coding genes. We show that the high amount of orphan genes is not due to poor sequence or assemble quality: 84% of the contig sequences contains an open reading frame with a start codon and E. crypticus homologs were identified for 92% of the core eukaryotic genes. Moreover, 65 and 77% of the unknown singletons and contigs, respectively, showed transcriptional activity. An Agilent 180K microarray platform was designed and validated by hybridizing cDNA from 3 day zinc- exposed E. crypticus to the concentration corresponding to 50% reduction in reproduction (EC50). Overall, 70% of all probes exerted a hybridization signal above background level. More specifically, the probes derived from contigs showed a wider range of average intensities when compared to probes derived from singletons. In total, 522 significantly regulated transcripts were identifying upon zinc exposure. Several significantly regulated genes exerted predicted functions (e.g. zinc efflux, zinc transport) associated with zinc stress. Unexpectedly, the microarray data suggest that zinc exposure alters retrotransposon activity in the E. crypticus genome. In conclusion, characterization of the presented E. crypticus transcriptome and associated microarray platform is a valuable and high quality resource that permits further functional genomics experiments examining gene expression patterns underlying distinct environmental stress conditions. We show that unknown sequences are not the result of technical errors but mostly represent functional genes that are actively transcribed.
2014-05-01 | GSE51838 | GEO
Project description:The soil worm Enchytraeus crypticus (oligochaete) is an ecotoxicology model species although without genome or transcriptome sequence information. The present research aimed at studying, via high-throughput pyrosequencing, the transcriptome of Enchytraeus crypticus, sampled from multiple test conditions, and the construction of a high-density microarray for functional genomic studies. A pyrosequencing run retrieved approximately 1.5 million reads representing 645 million bases. After assembly, 27,296 contigs and 87,686 singletons were obtained. from which 44% and 25% were annotated as protein-coding genes. We show that the high amount of orphan genes is not due to poor sequence or assemble quality: 84% of the contig sequences contains an open reading frame with a start codon and E. crypticus homologs were identified for 92% of the core eukaryotic genes. Moreover, 65 and 77% of the unknown singletons and contigs, respectively, showed transcriptional activity. An Agilent 180K microarray platform was designed and validated by hybridizing cDNA from 3 day zinc- exposed E. crypticus to the concentration corresponding to 50% reduction in reproduction (EC50). Overall, 70% of all probes exerted a hybridization signal above background level. More specifically, the probes derived from contigs showed a wider range of average intensities when compared to probes derived from singletons. In total, 522 significantly regulated transcripts were identifying upon zinc exposure. Several significantly regulated genes exerted predicted functions (e.g. zinc efflux, zinc transport) associated with zinc stress. Unexpectedly, the microarray data suggest that zinc exposure alters retrotransposon activity in the E. crypticus genome. In conclusion, characterization of the presented E. crypticus transcriptome and associated microarray platform is a valuable and high quality resource that permits further functional genomics experiments examining gene expression patterns underlying distinct environmental stress conditions. We show that unknown sequences are not the result of technical errors but mostly represent functional genes that are actively transcribed. The data presented in our manuscript is part of a larger experiment which was performed in single, large loop design. The analysis presented here can be replicated only by including all raw data from the larger experiment (all raw files are included in the archive linked to this submission). A single channel, interwoven loop design was used to test animals exposed to zinc EC50 on reproduction as compared to untreated controls for 4 days. 4 biological replicates per condition were used containing 25 grams of soil and 5 - 7, adult old animals per replicate. T4_con stands for untreated control soil while T4_50 are the samples exposed to EC50 of zinc on reproduction.
2014-05-01 | E-GEOD-51838 | biostudies-arrayexpress
Project description:Mechanisms of (photo)toxicity of TiO2 nanomaterials (NM103, NM104, NM105): using high-throughput gene expression in Enchytraeus crypticus
| PRJNA322344 | ENA
Project description:Negatives effects induced by exposure to ultra-violet (UV) radiation are well known. Nevertheless the modes of action of UV radiation are not well understood, in particular in soil invertebrates. In the present work, the effects of two UV doses (mimicking worst case scenarios in earth crust) on gene expression profile of Enchytraeus crypticus (Enchytraeidae, Oligochaeta) were investigated using the high-throughput 4 x 44K microarray developed for the species.
2017-06-13 | GSE69794 | GEO
Project description:Titanium dioxide (TiO2) based nanomaterials (NMs) are among the most produced NMs worldwide. When irradiated with light, particularly UV, TiO2 is photoactive, a property that is explored for several purposes. There is an increasingly number of reports on the negative effects of photoactivated TiO2 to non-target organisms. We have here studied the effect of a suite of reference type TiO2 NMs i.e. NM103, NM104, NM105 and compared these to the Bulk) with and without UV radiation to the oligochaete Enchytraeus crypticus. High-throughput gene expression was used to assess the molecular mechanisms, while also anchoring it to known effects at organism level (i.e., reproduction). Results showed that the photoactivity of TiO2 (UV exposed) played a major role in enhancing TiO2 toxicity, activating transcription of oxidative stress, lysosome damage and apoptosis mechanisms. For non-UV activated TiO2, where toxicity at organism level (reproduction) was lower, results showed the potential for long-term effects (i.e., mutagenic and epigenetic). NM specific mechanisms were identified: NM103 affected transcription and translation, NM104_UV negatively affected reproductive system/organs; and NM105_UV activated superoxide anion response. Results provided mechanistic information for UV-related phototoxicity of TiO2 materials and evidences of the potential long-term effects.
2018-11-07 | GSE81699 | GEO
Project description:Transcriptomic response of Enchytraeus crypticus exposed to a Fe-TiO2 dopped NM library
| PRJNA322325 | ENA
Project description:The effect of nanomaterials (NMs) is less understood in light of the implemented and existing methodologies for regular chemicals. To understand the mode of action of NMs is one of the alternatives to improve predictions and environmental risk assessment (ERA). In the present work the high-throughput gene expression tool (4x44K microarray for Enchytraeus crypticus) was used to investigate the mechanisms activated by Ni exposure. Ni nanoparticles (Ni-NPs) were investigated together with Ni-salt (NiNO3). Testing was done based on reproduction effect concentrations (EC20, EC50) using 3 and 7 days exposure periods.
2017-06-13 | GSE69793 | GEO
Project description:Enchytraeus crypticus strain:VU strain Transcriptome or Gene expression
| PRJNA207507 | ENA
Project description:Zinc (Zn) is known to be relatively toxic to some soil-living invertebrates including the ecologically important enchytraeid worms. To reveal the molecular mechanisms of zinc toxicity we assessed the gene expression profile of Enchytraeus crypticus (Enchytraeidae), exposed to the reproduction effect concentrations EC10 and EC50, over 4 consecutive days, using a high-throughput microarray (species customized). Three main mechanisms of toxicity to Zn were observed: 1) Zn trafficking (upregulation of zinc transporters, a defence response to regulate the cellular zinc level), 2) oxidative stress (variety of defence mechanisms, triggered by Reactive Oxygen Species (ROS) generated by Zn), and 3) effects on the nervous system (possibly the primary lesion explaining the avoidance behaviour and also why enchytraeids are relatively susceptible to Zn). The adverse outcome at the organism level (reproduction EC50) could be predicted based on gene expression (male gonad development, oocyte maturation), with Zn at the EC50 affecting processes related to higher stress levels. The gene expression response was time-specific and reflected the cascade of events taking place over-time. The 1 to 4 days of exposure design was a good strategy to capture the sequence of events towards zinc adverse outcomes in E. crypticus.
2022-02-21 | GSE183377 | GEO