The bowfin genome illuminates the developmental evolution of ray-finned fishes

Andrew W. Thompson; M. Brent Hawkins; Elise Parey; Dustin J. Wcisel; Tatsuya Ota; Kazuhiko Kawasaki; Emily Funk; Mauricio Losilla; Olivia E. Fitch; Qiaowei Pan; Romain Feron; Alexandra Louis; Jérôme Montfort; Marine Milhes; Brett L. Racicot; Kevin L. Childs; Quenton Fontenot; Allyse Ferrara; Solomon R. David; Amy R. McCune; Alex Dornburg; Jeffrey A. Yoder; Yann Guiguen; Hugues Roest Crollius; Camille Berthelot; Matthew P. Harris; Ingo Braasch

doi:10.1038/s41588-021-00914-y

The bowfin genome illuminates the developmental evolution of ray-finned fishes

Andrew W. Thompson, M. Brent Hawkins, Elise Parey, Dustin J. Wcisel, Tatsuya Ota, Kazuhiko Kawasaki, Emily Funk, Mauricio Losilla, Olivia E. Fitch, Qiaowei Pan, Romain Feron, Alexandra Louis, Jérôme Montfort, Marine Milhes, Brett L. Racicot, Kevin L. Childs, Quenton Fontenot, Allyse Ferrara, Solomon R. David, Amy R. McCuneAlex Dornburg, Jeffrey A. Yoder, Yann Guiguen, Hugues Roest Crollius, Camille Berthelot, Matthew P. Harris, Ingo Braasch

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Abstract

The bowfin (Amia calva) is a ray-finned fish that possesses a unique suite of ancestral and derived phenotypes, which are key to understanding vertebrate evolution. The phylogenetic position of bowfin as a representative of neopterygian fishes, its archetypical body plan and its unduplicated and slowly evolving genome make bowfin a central species for the genomic exploration of ray-finned fishes. Here we present a chromosome-level genome assembly for bowfin that enables gene-order analyses, settling long-debated neopterygian phylogenetic relationships. We examine chromatin accessibility and gene expression through bowfin development to investigate the evolution of immune, scale, respiratory and fin skeletal systems and identify hundreds of gene-regulatory loci conserved across vertebrates. These resources connect developmental evolution among bony fishes, further highlighting the bowfin’s importance for illuminating vertebrate biology and diversity in the genomic era.

Original language	English (US)
Pages (from-to)	1373-1384
Number of pages	12
Journal	Nature Genetics
Volume	53
Issue number	9
DOIs	https://doi.org/10.1038/s41588-021-00914-y
State	Published - Sep 2021
Externally published	Yes

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© 2021, The Author(s).

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Thompson, A. W., Hawkins, M. B., Parey, E., Wcisel, D. J., Ota, T., Kawasaki, K., Funk, E., Losilla, M., Fitch, O. E., Pan, Q., Feron, R., Louis, A., Montfort, J., Milhes, M., Racicot, B. L., Childs, K. L., Fontenot, Q., Ferrara, A., David, S. R., ... Braasch, I. (2021). The bowfin genome illuminates the developmental evolution of ray-finned fishes. Nature Genetics, 53(9), 1373-1384. https://doi.org/10.1038/s41588-021-00914-y

Thompson, AW, Hawkins, MB, Parey, E, Wcisel, DJ, Ota, T, Kawasaki, K, Funk, E, Losilla, M, Fitch, OE, Pan, Q, Feron, R, Louis, A, Montfort, J, Milhes, M, Racicot, BL, Childs, KL, Fontenot, Q, Ferrara, A, David, SR, McCune, AR, Dornburg, A, Yoder, JA, Guiguen, Y, Roest Crollius, H, Berthelot, C, Harris, MP & Braasch, I 2021, 'The bowfin genome illuminates the developmental evolution of ray-finned fishes', Nature Genetics, vol. 53, no. 9, pp. 1373-1384. https://doi.org/10.1038/s41588-021-00914-y

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abstract = "The bowfin (Amia calva) is a ray-finned fish that possesses a unique suite of ancestral and derived phenotypes, which are key to understanding vertebrate evolution. The phylogenetic position of bowfin as a representative of neopterygian fishes, its archetypical body plan and its unduplicated and slowly evolving genome make bowfin a central species for the genomic exploration of ray-finned fishes. Here we present a chromosome-level genome assembly for bowfin that enables gene-order analyses, settling long-debated neopterygian phylogenetic relationships. We examine chromatin accessibility and gene expression through bowfin development to investigate the evolution of immune, scale, respiratory and fin skeletal systems and identify hundreds of gene-regulatory loci conserved across vertebrates. These resources connect developmental evolution among bony fishes, further highlighting the bowfin{\textquoteright}s importance for illuminating vertebrate biology and diversity in the genomic era.",

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doi = "10.1038/s41588-021-00914-y",

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AU - Childs, Kevin L.

AU - Fontenot, Quenton

AU - Ferrara, Allyse

AU - David, Solomon R.

AU - McCune, Amy R.

AU - Dornburg, Alex

AU - Yoder, Jeffrey A.

AU - Guiguen, Yann

AU - Roest Crollius, Hugues

AU - Berthelot, Camille

AU - Harris, Matthew P.

AU - Braasch, Ingo

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The bowfin genome illuminates the developmental evolution of ray-finned fishes

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