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 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 contains the full fathead minnow (FHM) reference genome and annotation data as well all DNA sequencing data (PacBio long reads and Illumina paired-end reads) and RNA-seq data that were used to create the fathead minnow genome reference. This dataset is associated with the following publication: Martinson, J., D. Bencic, G. Toth, R. Flick, M. Kostich, M.J. See, D. Lattier, A. Biales, and W. Huang. De Novo Assembly of the Nearly Complete Fathead Minnow Reference Genome Reveals a Repetitive but Compact Genome. ENVIRONMENTAL TOXICOLOGY AND CHEMISTRY. Society of Environmental Toxicology and Chemistry, Pensacola, FL, USA, 41(2): 448-461, (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).

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).

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).

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).

Data associated with exposures of fathead minnows to varying concentrations of metformin and/or guanylurea. Includes three individual studies: ex vivo steroidogenesis assay, 96 h time course assay, 23 d reproduction assay. This dataset is associated with the following publication: Blackwell, B., G. Ankley, A. Biales, J. Cavallin, A. Cole, T. Collette, D. Ekman, R. Hofer, W. Huang, K. Jensen, M. Kahl, A. Kittelson, S. Romano, M. See, Q. Teng, C. Tilton, and D. Villeneuve. Effects of Metformin and its Metabolite Guanylurea on Fathead Minnow (Pimephales promelas) Reproduction (FY22 Manuscript). ENVIRONMENTAL TOXICOLOGY AND CHEMISTRY. Society of Environmental Toxicology and Chemistry, Pensacola, FL, USA, 41(11): 2708-2720, (2022).

This study demonstrates the potential of whole-mount in situ hybridization (WISH), in conjunction with quantitative real-time polymerase chain reaction (QPCR) assays, to examine the mechanistic basis of the effects of toxicants on early-lifestage fathead minnows. Specifically, fathead minnow embryos were exposed to the environmentally-relevant estrogen receptor agonist, estrone, and the data show that: (1) the estrogen-responsive gene transcripts esr1, vtg, and cyp19b can be up-regulated in very early-lifestages of the fathead minnow, (2) WISH methods developed for zebrafish can also be applied successfully to fathead minnows, and (3) WISH has potential to be a useful tool for toxicological studies pertaining to early-lifestage development in the fathead minnow. This type of mechanistic information relative to spatial distribution of gene expression is important in determining potential biological pathways that may be impacted by targeted chemicals and the development of associated adverse outcome pathways. This dataset is associated with the following publication: Cavallin, J., A. Schroeder, K. Jensen , D. Villeneuve , B. Blackwell, K. Carlson, M. Kahl , C. LaLone , E. Randolph , and G. Ankley. Evaluation of whole-mount in situ hybridization as a tool for pathway-based toxicological research with early-life stage fathead minnows. AQUATIC TOXICOLOGY. Elsevier Science Ltd, New York, NY, USA, 169: 19-26, (2015).

Genetic linkage maps are valuable tools in evolutionary biology; however, their availability for wild populations is extremely limited. Fundulus heteroclitus (Atlantic killifish) is a non-migratory estuarine fish that exhibits high allelic and phenotypic diversity partitioned among subpopulations that reside in disparate environmental conditions. An ideal candidate model organism for studying gene-environment interactions, the molecular toolbox for F. heteroclitus is limited. We identified hundreds of novel microsatellites which, when combined with existing microsatellites and single nucleotide polymorphisms (SNPs), were used to construct the first genetic linkage map for this species. By integrating independent linkage maps from three genetic crosses, we developed a consensus map containing 24 linkage groups, consistent with the number of chromosomes reported for this species. These linkage groups span 2300 centimorgans (cM) of recombinant genomic space, intermediate in size relative to the current linkage maps for the teleosts, medaka and zebrafish. Comparisons between fish genomes support a high degree of synteny between the consensus F. heteroclitus linkage map and the medaka and (to a lesser extent) zebrafish physical genome assemblies. This dataset is associated with the following publication: Waits , E., J. Martinson , B. Rinner, S. Morris, D. Proestou, D. Champlin , and D. Nacci. Genetic linkage map and comparative genome analysis for the estuarine Atlantic killifish (Fundulus heteroclitus). Open Journal of Genetics. Scientific Research Publishing, Inc., Irvine, CA, USA, 6: 28-38, (2016).