@article{0f460f4060a0440ab57933751cd5842f,
title = "The bowfin genome illuminates the developmental evolution of ray-finned fishes",
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.",
author = "Thompson, {Andrew W.} and Hawkins, {M. Brent} and Elise Parey and Wcisel, {Dustin J.} and Tatsuya Ota and Kazuhiko Kawasaki and Emily Funk and Mauricio Losilla and Fitch, {Olivia E.} and Qiaowei Pan and Romain Feron and Alexandra Louis and J{\'e}r{\^o}me Montfort and Marine Milhes and Racicot, {Brett L.} and Childs, {Kevin L.} and Quenton Fontenot and Allyse Ferrara and David, {Solomon R.} and McCune, {Amy R.} and Alex Dornburg and Yoder, {Jeffrey A.} and Yann Guiguen and {Roest Crollius}, Hugues and Camille Berthelot and Harris, {Matthew P.} and Ingo Braasch",
note = "Funding Information: We are thankful for grant support from NIH R01OD011116 (I.B.), NSF DDIG DEB-1600920 (M.B.H.), NSF IOS-1755242 (A.D.) and NSF IOS-1755330 (J.A.Y.). Parts of this work have been supported by the Agence Nationale de la Recherche, France (ANR GenoFish project, 2016-2021, ANR-16-CE12-0035) to H.R.C., C.B., E.P., A.L. and Y.G. E.P., C.B. and H.R.C. received support under the program {\textquoteleft}Investissements d{\textquoteright}Avenir{\textquoteright} launched by the French government and implemented by ANR with references ANR– 10–LABX–54 MEMOLIFE and ANR-10-IDEX-0001-02 PSL* Universit{\'e} Paris. We thank F. Feng for access to Oneida Lake bowfin spawning habitats, the Bauer Core at Harvard University for sequencing fin transcriptomes and M. Gundappa (FISH & LINES) for species illustrations. Species silhouettes were obtained from http://PhyloPic.org. We are exceedingly grateful to the late J.L. G{\'o}mez-Skarmeta for his guidance on establishing ATAC-seq in holosteans. Publisher Copyright: {\textcopyright} 2021, The Author(s).",
year = "2021",
month = sep,
doi = "10.1038/s41588-021-00914-y",
language = "English (US)",
volume = "53",
pages = "1373--1384",
journal = "Nature Genetics",
issn = "1061-4036",
publisher = "Nature Publishing Group",
number = "9",
}