The fathead minnow (Pimephales promelas) is a laboratory model organism widely used in regulatory toxicity testing and ecotoxicology research. Despite, the wealth of toxicological data for this organism, until recently genome scale information was lacking for the species, which limited the utility of the species for pathway-based toxicity testing and research. As part of a EPA Pathfinder Innovation Project, next generation sequencing was applied to generate a draft genome assembly, which was published in 2016. However, application of those genome-scale sequencing resources was still limited by the lack of available gene annotations for fathead minnow. Here we report on development of a first generation genome annotation for fathead minnow and the dissemination of that information through a web-based browser that makes it easy to search for genes of interest, extract the corresponding sequence, identify intron and exon boundaries and regulatory regions, and align the computationally predicted genes with other supporting evidence. This work greatly enhances the utility of the genome assemblies that were developed and makes it accessible to the ecotoxicology community world-wide, opening up a wide array of new research opportunities with the species. The URL associated with this data set provides access to the genome browser that was developed as well as the current gene models and evidence tracks. This dataset is associated with the following publication: Saari, T., A. Schroeder, G. Ankley, and D. Villeneuve. First generation annotations for the fathead minnow (Pimephales promelas) genome. ENVIRONMENTAL TOXICOLOGY AND CHEMISTRY. Society of Environmental Toxicology and Chemistry, Pensacola, FL, USA, 36(12): 3436-3442, (2017).

The dataset provides the URLs for accessing the genome sequence data and two draft assemblies as well as fathead minnow genotyping data associated with estimating the heterozygosity of the in-bred line. This dataset is associated with the following publication: Burns, F., L. Cogburn, G. Ankley , D. Villeneuve , E. Waits , Y. Chang, V. Llaca, S. Deschamps, R. Jackson, and R. Hoke. Sequencing and De novo Draft Assemblies of the Fathead Minnow (Pimphales promelas)Reference Genome. ENVIRONMENTAL TOXICOLOGY AND CHEMISTRY. Society of Environmental Toxicology and Chemistry, Pensacola, FL, USA, 35(1): 212-217, (2016).

The dataset provides the URLs for accessing the genome sequence data and two draft assemblies as well as fathead minnow genotyping data associated with estimating the heterozygosity of the in-bred line. This dataset is associated with the following publication: Burns, F., L. Cogburn, G. Ankley , D. Villeneuve , E. Waits , Y. Chang, V. Llaca, S. Deschamps, R. Jackson, and R. Hoke. Sequencing and De novo Draft Assemblies of the Fathead Minnow (Pimphales promelas)Reference Genome. ENVIRONMENTAL TOXICOLOGY AND CHEMISTRY. Society of Environmental Toxicology and Chemistry, Pensacola, FL, USA, 35(1): 212-217, (2016).

The dataset includes survival of control, control injected, and CRISPR/Cas9 injected embryos as well as percent efficiency of insertion/deletion mutation formation for the three different CRISPR guide strands/targets evaluated in this study. This dataset is associated with the following publication: Maki, J., J. Cavallin, K. Lott, T. Saari, G. Ankley, and D. Villeneuve. A method for CRISPR/Cas9 mutation of genes in fathead minnow (Pimephales promelas). AQUATIC TOXICOLOGY. Elsevier Science Ltd, New York, NY, USA, 222: 12 pg., (2020).

This dataset presents the full hepatic transcriptomes of fathead minnows (Pimephales promelas) caged for four days at multiple sites within the Milwaukee Estuary area of concern and additional control sites. At these same sites over the same period of exposure, time integrated water samples were collected and assessed for the presence of over 170 relevant chemical analytes. Access to both full sequencing of fish samples as well as water contaminant data will allow others to explore the health of these ecosystems. This dataset is associated with the following publication: Garcia-Reyero, N., M. Arick II, A. Woolard, M. Wilbanks, J. Mylroie, K. Jensen, M. Kahl, D. Feifarek, S. Poole, E. Randolph, J. Cavallin, B. Blackwell, D. Villeneuve, G. Ankley, and E. Perkins. Male fathead minnow transcriptomes and associated chemical analytes in the Milwaukee estuary system. Scientific Data. Springer Nature, New York, NY, USA, 9: 476, (2022).

This dataset presents the full hepatic transcriptomes of fathead minnows (Pimephales promelas) caged for four days at multiple sites within the Milwaukee Estuary area of concern and additional control sites. At these same sites over the same period of exposure, time integrated water samples were collected and assessed for the presence of over 170 relevant chemical analytes. Access to both full sequencing of fish samples as well as water contaminant data will allow others to explore the health of these ecosystems. This dataset is associated with the following publication: Garcia-Reyero, N., M. Arick II, A. Woolard, M. Wilbanks, J. Mylroie, K. Jensen, M. Kahl, D. Feifarek, S. Poole, E. Randolph, J. Cavallin, B. Blackwell, D. Villeneuve, G. Ankley, and E. Perkins. Male fathead minnow transcriptomes and associated chemical analytes in the Milwaukee estuary system. Scientific Data. Springer Nature, New York, NY, USA, 9: 476, (2022).

Given that larval fish stages provide opportunities for development of stressor-selective screening level tests, this work aimed to investigate the optimal age of fathead minnow larva and duration of exposure for the pharmaceutical, propranolol, found in the environment. Differentially expressed genes were studied as well as gene set enrichment analysis. This dataset is associated with the following publication: Biales, A., D. Bencic, R. Flick, and G. Toth. 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. Society of Environmental Toxicology and Chemistry, Pensacola, FL, USA, 43(4): 807-820, (2024).

The present study describes pilot testing of a high throughput compatible transcriptomics assay with larval fathead minnows. One day post hatch fathead minnows were exposed to eleven different concentrations of three metals, three selective serotonin reuptake inhibitors, and four neonicotinoid-like compounds for 24 h and concentration response modeling was applied to whole body gene expression data. Transcriptomics-based points of departure (tPODs) were consistently lower than effect concentrations reported in apical endpoint studies in fish. However, larval fathead minnow-based tPODs were not always lower than concentrations reported to elicit apical toxicity in other aquatic organisms like crustaceans or insects. Random in silico subsampling of data from the pilot assays was used to evaluate various assay design and acceptance considerations such as transcriptome coverage, number of replicate individuals to sequence per treatment, and minimum number of differentially expressed genes to produce a reliable tPOD estimate. This dataset is associated with the following publication: Villeneuve, D., M. Le, M. Hazemi, A. Biales, D. Bencic, K. Bush, R. Flick, J. Martinson, M. Morshead, K. Santana Rodriguez, K. Vitense, and K. Flynn. Pilot testing and optimization of a larval fathead minnow high throughput transcriptomics assay. Current Research in Toxicology. Elsevier B.V., Amsterdam, NETHERLANDS, 4: 100099, (2022).

The present study describes pilot testing of a high throughput compatible transcriptomics assay with larval fathead minnows. One day post hatch fathead minnows were exposed to eleven different concentrations of three metals, three selective serotonin reuptake inhibitors, and four neonicotinoid-like compounds for 24 h and concentration response modeling was applied to whole body gene expression data. Transcriptomics-based points of departure (tPODs) were consistently lower than effect concentrations reported in apical endpoint studies in fish. However, larval fathead minnow-based tPODs were not always lower than concentrations reported to elicit apical toxicity in other aquatic organisms like crustaceans or insects. Random in silico subsampling of data from the pilot assays was used to evaluate various assay design and acceptance considerations such as transcriptome coverage, number of replicate individuals to sequence per treatment, and minimum number of differentially expressed genes to produce a reliable tPOD estimate. This dataset is associated with the following publication: Villeneuve, D., M. Le, M. Hazemi, A. Biales, D. Bencic, K. Bush, R. Flick, J. Martinson, M. Morshead, K. Santana Rodriguez, K. Vitense, and K. Flynn. Pilot testing and optimization of a larval fathead minnow high throughput transcriptomics assay. Current Research in Toxicology. Elsevier B.V., Amsterdam, NETHERLANDS, 4: 100099, (2022).

The fathead minnow (Pimephales promelas) is a key model of vertebrate toxicity. Standardized tests of toxicity in fathead minnow have been developed to support regulatory science, and much is known about the response of the species to various environmental pollutants. However, there is little data on genetic variation within the species, despite the potential influence of genetic background on toxicological outcomes. Furthermore, the phylogenetic relationships among Pimephales species are not fully established and rates of evolutionary divergence within the species and genus have not been investigated. This study examined patterns of genetic variation across the genome within a single wild population of fathead minnow from the San Juan River of the southwestern U.S. These patterns were contrasted with variation in an inbred, captive population reared by the U.S. Environmental Protection Agency. The study also examined variation in two specimens each of the congeners bluntnose minnow (P. notatus), slim minnow (P. tenellus), and the bullhead minnow (P. vigilax). This data release describes the availability of the raw sequence data, the methods for identifying genetic polymorphisms among the samples, and provides the called polymorphisms in a standardized format (the variant call format, or VCF).