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De novo assembly and annotation of a highly contiguous reference genome of the fathead minnow (Pimephales promelas) reveals an AT-rich repetitive genome with compact gene structure

John Martinson, David C. Bencic, Gregory P. Toth, Mitchell S. Kostich, Robert W. Flick, Mary J. See, David Lattier, Adam D. Biales, View ORCID ProfileWeichun Huang
doi: https://doi.org/10.1101/2021.02.24.432777
John Martinson
1US Environmental Protection Agency, Molecular Indicators Branch, Center for Computational Toxicology and Exposure, Cincinnati, OH 45268, USA
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David C. Bencic
1US Environmental Protection Agency, Molecular Indicators Branch, Center for Computational Toxicology and Exposure, Cincinnati, OH 45268, USA
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Gregory P. Toth
1US Environmental Protection Agency, Molecular Indicators Branch, Center for Computational Toxicology and Exposure, Cincinnati, OH 45268, USA
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Mitchell S. Kostich
1US Environmental Protection Agency, Molecular Indicators Branch, Center for Computational Toxicology and Exposure, Cincinnati, OH 45268, USA
3Present Address: the Jackson laboratory for genomic medicine, Farmington, CT 06032, USA
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Robert W. Flick
1US Environmental Protection Agency, Molecular Indicators Branch, Center for Computational Toxicology and Exposure, Cincinnati, OH 45268, USA
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Mary J. See
1US Environmental Protection Agency, Molecular Indicators Branch, Center for Computational Toxicology and Exposure, Cincinnati, OH 45268, USA
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David Lattier
1US Environmental Protection Agency, Molecular Indicators Branch, Center for Computational Toxicology and Exposure, Cincinnati, OH 45268, USA
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Adam D. Biales
1US Environmental Protection Agency, Molecular Indicators Branch, Center for Computational Toxicology and Exposure, Cincinnati, OH 45268, USA
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  • For correspondence: huang.weichun@epa.gov biales.adam@epa.gov
Weichun Huang
2US Environmental Protection Agency, Molecular Indicators Branch, Center for Computational Toxicology and Exposure, Research Triangle Park, NC 27709, USA
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  • ORCID record for Weichun Huang
  • For correspondence: huang.weichun@epa.gov biales.adam@epa.gov
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ABSTRACT

The Fathead Minnow (FHM) is one of the most important and widely used model organisms in aquatic toxicology. The lack of a high-quality and well-annotated FHM reference genome, however, has severely hampered the efforts using modem ‘omics approaches with FHM for environmental toxicogenomics studies. We present here a de novo assembled and nearly complete reference of the fathead minnow genome. Compared to the current fragmented and sparsely annotated FHM genome assembly (FHM1), the new highly contiguous and well-annotated FHM reference genome (FHM2) represents a major improvement, having 95.1% of the complete BUSCOs (Benchmarking Universal Single-Copy Orthologs) and a scaffold N50 of 12.0 Mbps. The completeness of gene annotation for the FHM2 reference genome was demonstrated to be comparable to that of the zebrafish (ZF) GRCz11 reference genome. In addition, our comparative genomics analyses between FHM and ZF revealed highly conserved coding regions between two species while discovering much more compact gene structure in FHM than ZF. This study not only provides insights for assembling a highly repetitive AT-rich genome, but also delivers a critical genomic resource essential for toxicogenomics studies in environmental toxicology.

Competing Interest Statement

The authors have declared no competing interest.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-ND 4.0 International license.
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Posted February 25, 2021.
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De novo assembly and annotation of a highly contiguous reference genome of the fathead minnow (Pimephales promelas) reveals an AT-rich repetitive genome with compact gene structure
John Martinson, David C. Bencic, Gregory P. Toth, Mitchell S. Kostich, Robert W. Flick, Mary J. See, David Lattier, Adam D. Biales, Weichun Huang
bioRxiv 2021.02.24.432777; doi: https://doi.org/10.1101/2021.02.24.432777
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De novo assembly and annotation of a highly contiguous reference genome of the fathead minnow (Pimephales promelas) reveals an AT-rich repetitive genome with compact gene structure
John Martinson, David C. Bencic, Gregory P. Toth, Mitchell S. Kostich, Robert W. Flick, Mary J. See, David Lattier, Adam D. Biales, Weichun Huang
bioRxiv 2021.02.24.432777; doi: https://doi.org/10.1101/2021.02.24.432777

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