Data on genome annotation and analysis of earthworm Eisenia fetida.
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ABSTRACT:
SUBMITTER: Paul S
PROVIDER: S-EPMC6126081 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:In annelid worms, the nerve cord serves as a crucial organ to control the sensory and behavioral physiology. The inadequate genome resource of earthworms has prioritized the comprehensive analysis of their transcriptome dataset to monitor the genes express in the nerve cord and predict their role in the neurotransmission and sensory perception of the species. The present study focuses on identifying the potential transcripts and predicting their functional features by annotating the transcriptome dataset of nerve cord tissues prepared by Gong et al., 2010 from the earthworm Eisenia fetida. Totally 9762 transcripts were successfully annotated against the NCBI nr database using the BLASTX algorithm and among them 7680 transcripts were assigned to a total of 44,354 GO terms. The conserve domain analysis indicated the over representation of P-loop NTPase domain and calcium binding EF-hand domain. The COG functional annotation classified 5860 transcript sequences into 25 functional categories. Further, 4502 contig sequences were found to map with 124 KEGG pathways. The annotated contig dataset exhibited 22 crucial neuropeptides having considerable matches to the marine annelid Platynereis dumerilii, suggesting their possible role in neurotransmission and neuromodulation. In addition, 108 human stem cell marker homologs were identified including the crucial epigenetic regulators, transcriptional repressors and cell cycle regulators, which may contribute to the neuronal and segmental regeneration. The complete functional annotation of this nerve cord transcriptome can be further utilized to interpret genetic and molecular mechanisms associated with neuronal development, nervous system regeneration and nerve cord function.
| S-EPMC5688751 | biostudies-literature
Project description:Eisenia fetida, commonly known as red wiggler or compost worm, belongs to the Lumbricidae family of the Annelida phylum. Little is known about its genome sequence although it has been extensively used as a test organism in terrestrial ecotoxicology. In order to understand its gene expression response to environmental contaminants, we cloned 4032 cDNAs or expressed sequence tags (ESTs) from two E. fetida libraries enriched with genes responsive to ten ordnance related compounds using suppressive subtractive hybridization-PCR.A total of 3144 good quality ESTs (GenBank dbEST accession number EH669363-EH672369 and EL515444-EL515580) were obtained from the raw clone sequences after cleaning. Clustering analysis yielded 2231 unique sequences including 448 contigs (from 1361 ESTs) and 1783 singletons. Comparative genomic analysis showed that 743 or 33% of the unique sequences shared high similarity with existing genes in the GenBank nr database. Provisional function annotation assigned 830 Gene Ontology terms to 517 unique sequences based on their homology with the annotated genomes of four model organisms Drosophila melanogaster, Mus musculus, Saccharomyces cerevisiae, and Caenorhabditis elegans. Seven percent of the unique sequences were further mapped to 99 Kyoto Encyclopedia of Genes and Genomes pathways based on their matching Enzyme Commission numbers. All the information is stored and retrievable at a highly performed, web-based and user-friendly relational database called EST model database or ESTMD version 2.The ESTMD containing the sequence and annotation information of 4032 E. fetida ESTs is publicly accessible at http://mcbc.usm.edu/estmd/.
| S-EPMC2099499 | biostudies-literature
Project description:Timing and scope of genomic expansion within Annelida: evidence from Hoxeobox genes in the genome of the earthworm Eisenia fetida
| PRJEB10048 | ENA
Project description:The lumbricid earthworms (annelid family Lumbricidae) harbor gram-negative bacteria in their excretory organs, the nephridia. Comparative 16S rRNA gene sequencing of bacteria associated with the nephridia of several earthworm species has shown that each species of worm harbors a distinct bacterial species and that the bacteria from different species form a monophyletic cluster within the genus Acidovorax, suggesting that there is a specific association resulting from radiation from a common bacterial ancestor. Previous microscopy and culture studies revealed the presence of bacteria within the egg capsules and on the surface of embryos but did not demonstrate that the bacteria within the egg capsule were the same bacteria that colonized the nephridia. We present evidence, based on curing experiments, in situ hybridizations with Acidovorax-specific probes, and 16S rRNA gene sequence analysis, that the egg capsules contain high numbers of the bacterial symbiont and that juveniles are colonized during development within the egg capsule. Studies exposing aposymbiotic hatchlings to colonized adults and their bedding material suggested that juvenile earthworms do not readily acquire bacteria from the soil after hatching but must be colonized during development by bacteria deposited in the egg capsule. Whether this is due to the developmental stage of the host or the physiological state of the symbiont remains to be investigated.
| S-EPMC1352274 | biostudies-literature
Project description:The earthworm Eisenia fetida is one of the most used species in standardized soil ecotoxicity tests. Endpoints such as survival, growth and reproduction are ecologically relevant but provide little mechanistic insight into the toxicity pathways, especially at the molecular level. To better understand toxicological modes of action and to facilitate the development of molecular biomarkers, we have obtained 30,245 unique EST sequences from E. fetida and have designed a novel microarray with 15,119 60-mer oligonucleotide probes. These probes target the unique non-redundant EST sequences identified in E. fetida. Using this array we have profiled gene expression of E. fetida after exposure to CL-20, a cage cyclic nitramine previously found exhibiting reversible neurotoxicity to worms. Worms were exposed for 6 days to CL-20. Half of the exposed worms were allowed to recover in a clean environment for 7 days. Electrophysiological analysis showed that the conduction velocity of worm medial giant nerve fiber was significantly decreased after 6-d exposure to CL-20, and that giant nerve fiber function was restored at the end of the 7-d recovery period. Total RNA samples isolated from four treatment groups (6 replicates per group), i.e., 6-d control, 6-d exposed, 13-d control and 6-d exposed with 7-d recovery, were analyzed using the new 15K oligo array. Bioinformatics and statistical analyses have identified specific neurological pathways affected by CL-20 and recovery of these pathways after CL-20 removal. These results provide significant insights on the CL-20 toxic mode of action and how earthworms can recover from chemical stressors.
2009-10-14 | GSE18536 | GEO
Project description:BackgroundExplosive compounds such as TNT and RDX are recalcitrant contaminants often found co-existing in the environment. In order to understand the joint effects of TNT and RDX on earthworms, an important ecological and bioindicator species at the molecular level, we sampled worms (Eisenia fetida) exposed singly or jointly to TNT (50 mg/kg soil) and RDX (30 mg/kg soil) for 28 days and profiled gene expression in an interwoven loop designed microarray experiment using a 4k-cDNA array. Lethality, growth and reproductive endpoints were measured.ResultsSublethal doses of TNT and RDX had no significant effects on the survival and growth of earthworms, but significantly reduced cocoon and juvenile counts. The mixture exhibited more pronounced reproductive toxicity than each single compound, suggesting an additive interaction between the two compounds. In comparison with the controls, we identified 321 differentially expressed transcripts in TNT treated worms, 32 in RDX treated worms, and only 6 in mixture treated worms. Of the 329 unique differentially expressed transcripts, 294 were affected only by TNT, 24 were common to both TNT and RDX treatments, and 3 were common to all treatments. The reduced effects on gene expression in the mixture exposure suggest that RDX might interact in an antagonistic manner with TNT at the gene expression level. The disagreement between gene expression and reproduction results may be attributed to sampling time, absence of known reproduction-related genes, and lack of functional information for many differentially expressed transcripts. A gene potentially related to reproduction (echinonectin) was significantly depressed in TNT or RDX exposed worms and may be linked to reduced fecundity.ConclusionsSublethal doses of TNT and RDX affected many biological pathways from innate immune response to oogenesis, leading to reduced reproduction without affecting survival and growth. A complex interaction between mixtures of RDX and TNT was observed at the gene expression level that requires further study of the dynamics of gene expression and reproductive activities in E. fetida. These efforts will be essential to gain an understanding of the additive reproductive toxicity between RDX and TNT.
| S-EPMC2386057 | biostudies-literature
Project description:Survival of earthworms in the environment depends on their ability to recognize and eliminate potential pathogens. This work is aimed to compare the innate defense mechanisms of two closely related earthworm species, Eisenia andrei and Eisenia fetida, that inhabit substantially different ecological niches. While E. andrei lives in a compost and manure, E. fetida can be found in the litter layer in forests. Therefore, the influence of environment-specific microbiota on the immune response of both species was followed. Firstly, a reliable method to discern between E. andrei and E. fetida based on species-specific primers for cytochrome c oxidase I (COI) and stringent PCR conditions was developed. Secondly, to analyze the immunological profile in both earthworm species, the activity and expression of lysozyme, pattern recognition protein CCF, and antimicrobial proteins with hemolytic function, fetidin and lysenins, have been assessed. Whereas, CCF and lysozyme showed only slight differences in the expression and activity, fetidin/lysenins expression as well as the hemolytic activity was considerably higher in E. andrei as compared to E. fetida. The expression of fetidin/lysenins in E. fetida was not affected upon the challenge with compost microbiota, suggesting more substantial changes in the regulation of the gene expression. Genomic DNA analyses revealed significantly higher level of fetidin/lysenins (determined using universal primer pairs) in E. andrei compared to E. fetida. It can be hypothesized that E. andrei colonizing compost as a new habitat acquired an evolutionary selection advantage resulting in a higher expression of antimicrobial proteins.
| S-EPMC3815151 | biostudies-literature
Project description:The earthworm Eisenia fetida is one of the most used species in standardized soil ecotoxicity tests. Endpoints such as survival, growth and reproduction are ecologically relevant but provide little mechanistic insight into the toxicity pathways, especially at the molecular level. To better understand toxicological modes of action and to facilitate the development of molecular biomarkers, we have obtained 30,245 unique EST sequences from E. fetida and have designed a novel microarray with 15,119 60-mer oligonucleotide probes. These probes target the unique non-redundant EST sequences identified in E. fetida. Using this array we have profiled gene expression of E. fetida after exposure to CL-20, a cage cyclic nitramine previously found exhibiting reversible neurotoxicity to worms. Worms were exposed for 6 days to CL-20. Half of the exposed worms were allowed to recover in a clean environment for 7 days. Electrophysiological analysis showed that the conduction velocity of worm medial giant nerve fiber was significantly decreased after 6-d exposure to CL-20, and that giant nerve fiber function was restored at the end of the 7-d recovery period. Total RNA samples isolated from four treatment groups (6 replicates per group), i.e., 6-d control, 6-d exposed, 13-d control and 6-d exposed with 7-d recovery, were analyzed using the new 15K oligo array. Bioinformatics and statistical analyses have identified specific neurological pathways affected by CL-20 and recovery of these pathways after CL-20 removal. These results provide significant insights on the CL-20 toxic mode of action and how earthworms can recover from chemical stressors. Adult earthworms (E. fetida) were exposed on filter paper to CL-20 (0.2 ug/cm2) for 6 days with or without 7-day recovery (4 treatment groups in total). Each treatment group had 9 replicate worms, six of which were used for gene expression analysis. Worms were measured for their medial giant nerve fiber conduction velocity using a non-invasive electrophysiological technique immediately before takedown. At the termination of the 6-d or 13-d experiment, worms were snap-frozen and fixed in RNAlater-ICE. Total RNA was isolated from the fixed worms. A total of 24 worm RNA samples were hybridized to three 8x15K custom-designed Agilent oligo arrays using Agilentâs one-color Low RNA Input Linear Amplification Kit. The array contains 15,208 non-redundant 60-mer probes, each targeting a unique E. fetida transcript. After hybridization and scanning, gene expression data were acquired using GenePix Pro 6.0.
2009-10-14 | E-GEOD-18536 | biostudies-arrayexpress
Project description:Annelida represents a large and morphologically diverse group of bilaterian organisms. The recently published polychaete and leech genome sequences revealed an equally dynamic range of diversity at the genomic level. The availability of more annelid genomes will allow for the identification of evolutionary genomic events that helped shape the annelid lineage and better understand the diversity within the group. We sequenced and assembled the genome of the common earthworm, Eisenia fetida. As a first pass at understanding the diversity within the group, we classified 363 earthworm homeoboxes and compared them with those of the leech Helobdella robusta and the polychaete Capitella teleta. We inferred many gene expansions occurring in the lineage connecting the most recent common ancestor (MRCA) of Capitella and Eisenia to the Eisenia/Helobdella MRCA. Likewise, the lineage leading from the Eisenia/Helobdella MRCA to the leech H. robusta has experienced substantial gains and losses. However, the lineage leading from Eisenia/Helobdella MRCA to E. fetida is characterized by extraordinary levels of homeobox gain. The evolutionary dynamics observed in the homeoboxes of these lineages are very likely to be generalizable to all genes. These genome expansions and losses have likely contributed to the remarkable biology exhibited in this group. These results provide a new perspective from which to understand the diversity within these lineages, show the utility of sub-draft genome assemblies for understanding genomic evolution, and provide a critical resource from which the biology of these animals can be studied.
| S-EPMC4758240 | biostudies-literature
Project description:1H NMR-based metabolomics was used to measure the response of Eisenia fetida earthworms after exposure to sub-lethal concentrations of perfluorooctane sulfonate (PFOS) in soil. Earthworms were exposed to a range of PFOS concentrations (five, 10, 25, 50, 100 or 150 mg/kg) for two, seven and fourteen days. Earthworm tissues were extracted and analyzed by 1H NMR. Multivariate statistical analysis of the metabolic response of E. fetida to PFOS exposure identified time-dependent responses that were comprised of two separate modes of action: a non-polar narcosis type mechanism after two days of exposure and increased fatty acid oxidation after seven and fourteen days of exposure. Univariate statistical analysis revealed that 2-hexyl-5-ethyl-3-furansulfonate (HEFS), betaine, leucine, arginine, glutamate, maltose and ATP are potential indicators of PFOS exposure, as the concentrations of these metabolites fluctuated significantly. Overall, NMR-based metabolomic analysis suggests elevated fatty acid oxidation, disruption in energy metabolism and biological membrane structure and a possible interruption of ATP synthesis. These conclusions obtained from analysis of the metabolic profile in response to sub-lethal PFOS exposure indicates that NMR-based metabolomics is an excellent discovery tool when the mode of action (MOA) of contaminants is not clearly defined.
| S-EPMC3901287 | biostudies-literature