ArticleEnvironmental toxicology and chemistry2022
De Novo Assembly of the Nearly Complete Fathead Minnow Reference Genome Reveals a Repetitive but Compact Genome.
Article in Environmental toxicology and chemistry, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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Who cites it
12 citing papers in PubMed, 24 citations in OpenAlex.
- A chromosome-level genome assembly of Hemibarbus maculatus.Scientific data · 2026Article
- Bioactivity of the ubiquitous tire preservative 6PPD and degradant, 6PPD-quinone in fish- and mammalian-based assays.Toxicological sciences : an official journal of the Society of Toxicology · 2025Article
- Article
- Assembly and annotation of a chromosome-level reference genome for the endangered Colorado pikeminnow (Ptychocheilus lucius).G3 (Bethesda, Md.) · 2024Article
- The Highly Repetitive Genome of Myxobolus rasmusseni, an Emerging Myxozoan Parasite of Fathead Minnows.Genome biology and evolution · 2024Article
- Comparing Transcriptomic Points of Departure to Apical Effect Concentrations For Larval Fathead Minnow Exposed to Chemicals with Four Different Modes Of Action.Archives of environmental contamination and toxicology · 2024Article
- Effects of Age and Exposure Duration on the Sensitivity of Early Life Stage Fathead Minnow (Pimephales promelas) to Waterborne Propranolol Exposure.Environmental toxicology and chemistry · 2024Article
- A high-quality reference genome for the common creek chub, Semotilus atromaculatus.G3 (Bethesda, Md.) · 2024Article
- Article
- Pilot testing and optimization of a larval fathead minnow high throughput transcriptomics assay.Current research in toxicology · 2023Article
- Effects of Metformin and its Metabolite Guanylurea on Fathead Minnow (Pimephales promelas) Reproduction.Environmental toxicology and chemistry · 2022Article
- Genome resequencing clarifies phylogeny and reveals patterns of selection in the toxicogenomics modelPeerJ · 2022Article
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Authors and funding
9 authors at 1 institution in 1 country.
Funding
Abstract
The fathead minnow is a widely used model organism in environmental toxicology. The lack of a high-quality fathead minnow reference genome, however, has severely hampered its uses in toxicogenomics. We present the de novo assembly and annotation of the fathead minnow genome using long PacBio reads, Bionano and Hi-C scaffolding data, and large RNA-sequencing data sets from different tissues and life stages. The new annotated fathead minnow reference genome has a scaffold N50 of 12.0 Mbp and a complete benchmarking universal single-copy orthologs score of 95.1%. The completeness of annotation for the new reference genome is comparable to that of the zebrafish GRCz11 reference genome. The fathead minnow genome, revealed to be highly repetitive and sharing extensive syntenic regions with the zebrafish genome, has a much more compact gene structure than the zebrafish genome. Particularly, comparative genomic analysis with zebrafish, mouse, and human showed that fathead minnow homologous genes are relatively conserved in exon regions but had strikingly shorter intron regions. The new fathead minnow reference genome and annotation data, publicly available from the National Center for Biotechnology Information and the University of California Santa Cruz genome browser, provides an essential resource for aquatic toxicogenomic studies in ecotoxicology and public health. Environ Toxicol Chem 2022;41:448-461. Published 2021. This article is a U.S. Government work and is in the public domain in the USA.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.