Dataset Information

Annotation of nerve cord transcriptome in earthworm Eisenia fetida.

ABSTRACT: 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.

SUBMITTER: Ponesakki V

PROVIDER: S-EPMC5688751 | biostudies-literature | 2017 Dec

REPOSITORIES: biostudies-literature

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Annotation of nerve cord transcriptome in earthworm <i>Eisenia fetida</i>.

Ponesakki Vasanthakumar V Paul Sayan S Mani Dinesh Kumar Sudalai DKS Rajendiran Veeraragavan V Kanniah Paulkumar P Sivasubramaniam Sudhakar S

Genomics data 20171012

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 transcriptom ...[more]

PMID: 29204349

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Project description:High density oligonucleotide probe arrays have increasingly become an important tool in genomics studies. In organisms with incomplete genome sequence, one strategy for oligo probe design is to reduce the number of unique probes that target every non-redundant transcript through bioinformatic analysis and experimental testing. Here we adopted this strategy in making oligo probes for the earthworm Eisenia fetida, a species for which we have sequenced transcriptome-scale expressed sequence tags (ESTs). Our objectives were to identify unique transcripts as targets, to select an optimal and non-redundant oligo probe for each of these target ESTs, and to annotate the selected target sequences. We developed a streamlined and easy-to-follow approach to the design, validation and annotation of species-specific array probes. Four 244K-formatted oligo arrays were designed using eArray and were hybridized to a pooled E. fetida cRNA sample. We identified 63,541 probes with unsaturated signal intensities consistently above the background level. Target transcripts of these probes were annotated using several sequence alignment algorithms. Significant hits were obtained for 37,439 (59%) probed targets. We validated and made publicly available 63.5K oligo probes so the earthworm research community can use them to pursue ecological, toxicological, and other functional genomics questions. Our approach is efficient, cost-effective and robust because it (1) does not require a major genomics core facility; (2) allows new probes to be easily added and old probes modified or eliminated when new sequence information becomes available, (3) is not bioinformatics-intensive upfront but does provide opportunities for more in-depth annotation of biological functions for target genes; and (4) if desired, EST orthologs to the UniGene clusters of a reference genome can be identified and selected in order to improve the target gene specificity of designed probes. This approach is particularly applicable to organisms with a wealth of EST sequences but unfinished genome.

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.

Project description:Biochar is the degradation-resistant product generated by the pyrolysis of organic materials and is produced for the intended use of land application in order to promote carbon sequestration and soil improvement. However, despite the many potential benefits biochar application offers, it is important to quantify any ecological impacts that may result from soil amendment in order to avoid potentially causing negative effects upon soil biota which are crucial in the many ecosystem services provided by soil. Any impacts on earthworms in particular are important to evaluate because of their pivotal role in organic matter breakdown, nutrient cycling and soil formation. In this study, we conducted a series of ecotoxicological assays to determine lethal and sublethal (avoidance, mass change and moisture content) effects of heavy biochar applications that reflect levels that may be used in soil restoration efforts. Two earthworm species, Eisenia fetida, an epigeic species, and Lumbricus terrestris, an anecic species, were utilised as test organisms. Two types of biochar, produced from wheat straw and rice husk feedstocks, respectively, were applied to OECD artificial soil and to a natural soil (Kettering loam) at rates of up to 20% w/w. The influence of biochar application on soil porewater chloride, fluoride and phosphate concentrations was also assessed. The biochar applications induced only a subtle level of avoidance behaviour while effects on survival over a 4-week exposure period were inconsistent. However, death and physical damage to some individual earthworms at high biochar application rates were observed, the mechanisms and processes leading to which should be investigated further. Earthworm development (mean mass change over time) proved to be a more sensitive measure, revealing negative effects on L. terrestris at 10% and 20% (w/w) wheat biochar applications in OECD soil and at 20% (w/w) applications of both biochars in Kettering loam. The moisture content of E. fetida remained remarkably consistent across all treatments (~ 82%), indicating that this is not a sensitive measure of effects. The high rates of biochar application resulted in increased chloride (2 to 3-fold) and phosphate (100-fold) concentrations in simulated soil porewaters, which has important implications for soil fertility and production but also for environmental management.

Dataset Information

Annotation of nerve cord transcriptome in earthworm Eisenia fetida.

Publications

Annotation of nerve cord transcriptome in earthworm <i>Eisenia fetida</i>.

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