Sequencing and de novo draft assemblies of a fathead minnow (<i>Pimephales promelas</i>) reference genome

Burns, Frank R.; Cogburn, Amarin; Ankley, Gerald T.; Villeneuve, Daniel L.; Waits, Eric R.; Chang, Yen‐Hsiang; Llaca, Víctor; Deschamps, Stéphane; Jackson, Raymond J.; Hoke, Robert A.

doi:10.1002/etc.3186

Cited by 29 publications

(29 citation statements)

References 37 publications

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“…The zebrafish, Danio rerio, is a model organism of scientific importance, and has been heavily studied in its development and its genome (Howe et al 2013). Advancement in sequencing technologies has also allowed the sequencing and publication of whole genome sequences of several cypriniforms (Burns et al 2015;Wang et al 2015;Xu et al 2014;Yang et al 2016).…”

Section: Introductionmentioning

confidence: 99%

Phylogenetic classification of extant genera of fishes of the order Cypriniformes (Teleostei: Ostariophysi)

Tan

Armbruster

2018

Zootaxa

154

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The order Cypriniformes is the most diverse order of freshwater fishes. Recent phylogenetic studies have approached a consensus on the phylogenetic relationships of Cypriniformes and proposed a new phylogenetic classification of familylevel groupings in Cypriniformes. The lack of a reference for the placement of genera amongst families has hampered the adoption of this phylogenetic classification more widely. We herein provide an updated compilation of the membership of genera to suprageneric taxa based on the latest phylogenetic classifications. We propose a new taxon: subfamily Esominae within Danionidae, for the genus Esomus.

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Section: Introductionmentioning

confidence: 99%

Phylogenetic classification of extant genera of fishes of the order Cypriniformes (Teleostei: Ostariophysi)

Tan

Armbruster

2018

Zootaxa

154

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“…Recent investigations of the fathead minnow have made the total genome available, and a fathead minnow genome browser has been launched (Saari et al 2017) with a sequenced 1.22-Gb-long genome and 226 mapped genes (Burns et al 2016). Although the fathead minnow is frequently used as ecotoxicological model organism, the considered transcriptomic microarray platforms cover only a small set of the total fathead minnow genome (Burns et al 2016). However, 2 platforms are based on sequences of the reference hepatic transcriptome (Wiseman et al 2013) and are annotated in the GenBank database (GPL17098 and GPL15775; Garcia-Reyero et al 2014).…”

Section: Resolution In Toxicogenomic Analysis: From Gene-wise Analysimentioning

confidence: 99%

A Self-Organizing Map of the Fathead Minnow Liver Transcriptome to Identify Consistent Toxicogenomic Patterns across Chemical Fingerprints

Krämer

Busch

Schüttler

2019

Environmental Toxicology and Chemistry

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Lack of consistent findings in different experimental settings remains a major challenge in toxicogenomics. The present study investigated whether consistency between findings of different microarray experiments can be improved when the analysis is based on a common reference frame (“toxicogenomic universe”), which can be generated using the machine learning algorithm of the self‐organizing map (SOM). This algorithm arranges and clusters genes on a 2‐dimensional grid according to their similarity in expression across all considered data. In the present study, 19 data sets, comprising of 54 different adult fathead minnow liver exposure experiments, were retrieved from Gene Expression Omnibus and used to train a SOM. The resulting toxicogenomic universe aggregates 58 872 probes to 2500 nodes and was used to project, visualize, and compare the fingerprints of these 54 different experiments. For example, we could identify a common pattern, with 14% of significantly regulated nodes in common, in the data sets of an interlaboratory study of ethinylestradiol exposures. Consistency could be improved compared with the 5% total overlap in regulated genes reported before. Furthermore, we could determine a specific and consistent estrogen‐related pattern of differentially expressed nodes and clusters in the toxicogenomic universe by applying additional clustering steps and comparing all obtained fingerprints. Our study shows that the SOM‐based approach is useful for generating comparable toxicogenomic fingerprints and improving consistency between results of different experiments. Environ Toxicol Chem 2020;39:526–537. © 2019 The Authors. Environmental Toxicology and Chemistry published by Wiley Periodicals, Inc. on behalf of SETAC.

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“…The first FHM draft genome was published in 2016 ( 33 ) and was produced from Illumina sequencing at 120X coverage. The genome annotation was later improved, leading to a total of 43,345 gene predictions ( 34 ).…”

Section: Introductionmentioning

confidence: 99%

Tissue-Based Mapping of the Fathead Minnow (Pimephales promelas) Transcriptome and Proteome

et al. 2018

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Omics approaches are broadly used to explore endocrine and toxicity-related pathways and functions. Nevertheless, there is still a significant gap in knowledge in terms of understanding the endocrine system and its numerous connections and intricate feedback loops, especially in non-model organisms. The fathead minnow (Pimephales promelas) is a widely used small fish model for aquatic toxicology and regulatory testing, particularly in North America. A draft genome has been published, but the amount of available genomic or transcriptomic information is still far behind that of other more broadly studied species, such as the zebrafish. Here, we used a proteogenomics approach to survey the tissue-specific proteome and transcriptome profiles in adult male fathead minnow. To do so, we generated a draft transcriptome using short and long sequencing reads from liver, testis, brain, heart, gill, head kidney, trunk kidney, and gastrointestinal tract. We identified 30,378 different putative transcripts overall, with the assembled contigs ranging in size from 264 to over 9,720 nts. Over 17,000 transcripts were >1,000 nts, suggesting a robust transcriptome that can be used to interpret RNA sequencing data in the future. We also performed RNA sequencing and proteomics analysis on four tissues, including the telencephalon, hypothalamus, liver, and gastrointestinal tract of male fish. Transcripts ranged from 0 to 600,000 copies per gene and a large portion were expressed in a tissue-specific manner. Specifically, the telencephalon and hypothalamus shared the most expressed genes, while the gastrointestinal tract and the liver were quite distinct. Using protein profiling techniques, we identified a total of 4,045 proteins in the four tissues investigated, and their tissue-specific expression pattern correlated with the transcripts at the pathway level. Similarly to the findings with the transcriptomic data, the hypothalamus and telencephalon had the highest degree of similarity in the proteins detected. The main purpose of this analysis was to generate tissue-specific omics data in order to support future aquatic ecotoxicogenomic and endocrine-related studies as well as to improve our understanding of the fathead minnow as an ecological model.

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Sequencing and de novo draft assemblies of a fathead minnow (Pimephales promelas) reference genome

Cited by 29 publications

References 37 publications

Phylogenetic classification of extant genera of fishes of the order Cypriniformes (Teleostei: Ostariophysi)

Phylogenetic classification of extant genera of fishes of the order Cypriniformes (Teleostei: Ostariophysi)

A Self-Organizing Map of the Fathead Minnow Liver Transcriptome to Identify Consistent Toxicogenomic Patterns across Chemical Fingerprints

Tissue-Based Mapping of the Fathead Minnow (Pimephales promelas) Transcriptome and Proteome

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