The central nervous system transcriptome of the weakly electric brown ghost knifefish (Apteronotus leptorhynchus): de novo assembly, annotation, and proteomics validation.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:25879418", "kind": "science-record", "revision": 7, "content_hash": "sha256:353130aba3bbbee73e4012bccdadaf83b68761db0381c25ec54e9f0c3bfaad32", "created_at": "2026-11-01T15:40:08Z", "updated_at": "2026-11-01T21:58:29Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "The central nervous system transcriptome of the weakly electric brown ghost knifefish (Apteronotus leptorhynchus): de novo assembly, annotation, and proteomics validation.", "doi": "10.1186/s12864-015-1354-2", "pmid": "25879418", "authors": ["Joseph P Salisbury", "Ruxandra F Sîrbulescu", "Benjamin M Moran", "Jared R Auclair", "Günther K H Zupanc", "Jeffrey N Agar"], "journal": "BMC genomics", "year": 2015, "abstract": "BACKGROUND: The brown ghost knifefish (Apteronotus leptorhynchus) is a weakly electric teleost fish of particular interest as a versatile model system for a variety of research areas in neuroscience and biology. The comprehensive information available on the neurophysiology and neuroanatomy of this organism has enabled significant advances in such areas as the study of the neural basis of behavior, the development of adult-born neurons in the central nervous system and their involvement in the regeneration of nervous tissue, as well as brain aging and senescence. Despite substantial scientific interest in this species, no genomic resources are currently available.\nRESULTS: Here, we report the de novo assembly and annotation of the A. leptorhynchus transcriptome. After evaluating several trimming and transcript reconstruction strategies, de novo assembly using Trinity uncovered 42,459 unique contigs containing at least a partial protein-coding sequence based on alignment to a reference set of known Actinopterygii sequences. As many as 11,847 of these contigs contained full or near-full length protein sequences, providing broad coverage of the proteome. A variety of non-coding RNA sequences were also identified and annotated, including conserved long intergenic non-coding RNA and other long non-coding RNA observed previously to be expressed in adult zebrafish (Danio rerio) brain, as well as a variety of miRNA, snRNA, and snoRNA. Shotgun proteomics confirmed translation of open reading frames from over 2,000 transcripts, including alternative splice variants. Assignment of tandem mass spectra was greatly improved by use of the assembly compared to databases of sequences from closely related organisms. The assembly and raw reads have been deposited at DDBJ/EMBL/GenBank under the accession number GBKR00000000. Tandem mass spectrometry data is available via ProteomeXchange with identifier PXD001285.\nCONCLUSIONS: Presented here is the first release of an annotated de novo transcriptome assembly from Apteronotus leptorhynchus, providing a broad overview of RNA expressed in central nervous system tissue. The assembly, which includes substantial coverage of a wide variety of both protein coding and non-coding transcripts, will allow the development of better tools to understand the mechanisms underlying unique characteristics of the knifefish model system, such as their tremendous regenerative capacity and negligible brain senescence.", "claims": [{"id": "claim-method", "statement": "Identifications were evaluated using MudPIT scoring, with a minimum peptide score of 20.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:25879418", "locator": "sections[20] \"LC-MS/MS and data analysis for protein identification\" paragraph 3", "quote": "Identifications were evaluated using MudPIT scoring, with a minimum peptide score of 20."}], "state": "complete"}, {"id": "claim-data-access", "statement": "This Transcriptome Shotgun Assembly project (BioProject ID PRJNA259518) has been deposited at DDBJ/EMBL/GenBank under the accession GBKR00000000. The version described in this paper is the first version, GBKR01000000. The mass spectrometry proteomics data have been deposited at the ProteomeXchange Consortium [121] via the PRIDE partner repository [122] with the dataset identifier PXD001285 and DOI 10.6019/PXD001285.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:25879418", "locator": "sections[21] \"Availability of supporting data\" paragraph 2", "quote": "This Transcriptome Shotgun Assembly project (BioProject ID PRJNA259518) has been deposited at DDBJ/EMBL/GenBank under the accession GBKR00000000. The version described in this paper is the first version, GBKR01000000. The mass spectrometry proteomics data have been deposited at the ProteomeXchange Consortium [121] via the PRIDE partner repository [122] with the dataset identifier PXD001285 and DOI 10.6019/PXD001285."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Using GOrilla minimum hypergeometric scoring on D. rerio Gene Ontology annotations for FPKM-ranked A. leptorhynchus assembly transcripts aligned at ≥80% coverage to a reference protein, the authors found that ribosome structural components and translation factors were the most prominently enriched features.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:25879418", "locator": "sections[8] \"Transcriptome coverage assessment and enrichment analysis\" paragraph 4", "quote": "To assess which molecular categories were most highly expressed among those transcripts of the A. leptorhynchus assembly that aligned to ≥80% of a reference D. rerio protein, assembly transcripts were first ranked by FPKM, and the GO classification for the corresponding D. rerio genes was used to determine enrichment of the most highly expressed transcripts using GOrilla [86]."}, {"asset": "source:pmid:25879418", "locator": "sections[8] \"Transcriptome coverage assessment and enrichment analysis\" paragraph 4", "quote": "GOrilla uses the variable enrichment thresholding method of minimum hypergeometric scoring to determine GO enrichment from ranked gene lists, with significantly enriched GO categories found on average in the top 9.6% of genes (4.8% S.D.)."}, {"asset": "source:pmid:25879418", "locator": "sections[8] \"Transcriptome coverage assessment and enrichment analysis\" paragraph 4", "quote": "When considering the relative expression levels of transcripts with full or near-fully resolved ORFs, structural components of the ribosome and factors involved in translation were found to be most prominent (Figure 4, Additional file 4: Table S3), consistent with the observation that the ribosome was the cellular component that had the highest percentage of well-resolved genes."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Using GOrilla minimum hypergeometric scoring on D. rerio Gene Ontology annotations for FPKM-ranked A. leptorhynchus assembly transcripts aligned at ≥80% coverage to a reference protein, the authors found that ribosome structural components and translation factors were the most prominently enriched features.", "steps": [{"id": "read_published_estimate", "order": 1, "name": "Read the published estimate from the source", "kind": "other", "state": "complete", "blocked_on": null, "description": "The claim, method and evidence span published with the source article.", "duration_hours": null, "parameters": {}, "inputs": ["source:pmid:25879418"], "outputs": ["the published estimate and its evidence"], "instruments": [], "reagents": []}, {"id": "obtain_source_data", "order": 2, "name": "Obtain the source data from the named repository", "kind": "data-preparation", "state": "complete", "blocked_on": null, "description": "The GEO series accession resolves and its sample accessions are listed. 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