Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1046655 | ENA |
REPOSITORIES: ENA
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Project description:Performing proteomic studies on non-model organisms with little or no genomic information is still difficult. However, many specific processes and biochemical pathways occur only in species that are poorly characterized at the genomic level. For example, many plants can reproduce both sexually and asexually, the first one allowing the generation of new genotypes and the latter their fixation. Thus, both modes of reproduction are of great agronomic value. However, the molecular basis of asexual reproduction is not understood in any plant. In ferns, it combines the production of unreduced spores (diplospory) and the formation of sporophytes from somatic cells (apogamy). To set the basis to study these processes, we performed transcriptomics by next-generation sequencing (NGS) and shotgun proteomics by tandem mass spectrometry in the apogamous fern D. affinis ssp. affinis. For protein identification we used the public viridiplantae database (VPDB) to identify orthologous proteins from other plant species and new transcriptomics data to generate a “species-specific transcriptome database” (SSTDB). In total 1397 protein clusters with 5865 unique peptide sequences were identified (13 decoy proteins out of 1410, protFDR 0.93% on protein cluster level). We show that using a “species-specific transcriptome database” for protein identification increases the number of identified peptides almost four times compared to using only the publically available viridiplantae database. We identified homologs of proteins involved in reproduction of higher plants, including proteins with a potential role in apogamy.
2017-04-11 | PXD005423 | Pride
Project description:The project aims at unraveling the venom repertoire of the lesser banded hornet (Vespa affinis) and investigate the regimes of natural selection underpinning their venom evolution. The study also sheds light on the clinical repercussions of the V. affinis venom.
2023-03-10 | PXD037171 | Pride
Project description:Euthynnus affinis transcriptome sequencing project
| PRJDB11735 | ENA
Project description:Compared to freshwater ecosystems, the health status of estuarine waters remains little studied despite their importance for many species. They also represent a zone of interest for Human settlements that make them the final sink of pollution in both the water column and sediment. Once in sediments, pollutants could represent a threat to benthic as well as pelagic estuarine species through resuspension events. In the Seine estuary, the copepod Eurytemora affinis has been previously presented as a relevant species to assess resuspended sediment contamination through the use of fitness-related effects at the individual level. The aim of the present study was to use E. affinis copepods to assess estuarine sediment-derived elutriates toxicity using both a molecular (i.e. transcriptomics) and a behavioral approach. Two sites along the Seine estuary were sampled. They were both under anthropic pressures from the industrial-port activities or wastewater treatment plants (i.e. Tancarville) or agricultural pressure from freshwater affluent (i.e. Fatouville). The analysis of sediments used to prepare elutriates reveals that both sites have close contamination profiles. The transcriptomic analysis reveals that exposure to both sites triggers the dysregulation of genes involved in biological function as defense response, immunity, ecdysone pathway or neurotoxicity. This analysis also reveals a higher count of dysregulated genes in the Fatouville site compared to the Tancarville despite their close contamination profile. These results emphasize the sensitivity of this molecular approach to assess environmental matrix toxicity with E. affinis. The analysis of the swimming behavior of E. affinis did not highlight significant effects after both sites elutriate exposure. However, our strategy to assess E. affinis swimming behavior (i.e the combination of the DanioVision observation chamber and the EthoVision analysis software) allows the discrimination of basal swimming behavior in this species. Thus, it represents a promising standardized tool to assess copepods swimming behavior in ecotoxicological studies.
2024-09-30 | GSE235722 | GEO
Project description:Rhinolophus affinis Cochleae Transcriptome
| PRJNA644044 | ENA