The bowfin genome illuminates the developmental evolution of ray-finned fishes
Andrew Thompson
(1)
,
M. Brent Hawkins
(2, 3, 4)
,
Elise Parey
(5)
,
Dustin Wcisel
(6)
,
Tatsuya Ota
(7)
,
Kazuhiko Kawasaki
(8)
,
Emily Funk
(9, 10)
,
Mauricio Losilla
(1)
,
Olivia Fitch
(1)
,
Qiaowei Pan
(11)
,
Romain Feron
(11, 12)
,
Alexandra Louis
(5)
,
Jérôme Montfort
(13)
,
Marine Milhes
(14)
,
Brett Racicot
(1)
,
Kevin Childs
(1)
,
Quenton Fontenot
(15)
,
Allyse Ferrara
(15)
,
Solomon David
(15)
,
Amy Mccune
(9)
,
Alex Dornburg
(16)
,
Jeffrey Yoder
(6)
,
Yann Guiguen
(13)
,
Hugues Roest Crollius
(5)
,
Camille Berthelot
(5)
,
Matthew Harris
(2, 3)
,
Ingo Braasch
(1)
1
Michigan State University [East Lansing]
2 HMS - Harvard Medical School [Boston]
3 Boston Children's Hospital
4 Harvard University
5 IBENS - Institut de biologie de l'ENS Paris
6 NC State - North Carolina State University [Raleigh]
7 SOKENDAI - Graduate University for Advanced Studies [Hayama]
8 Penn State - Pennsylvania State University
9 Cornell University [New York]
10 UC Davis - University of California [Davis]
11 UNIL - Université de Lausanne = University of Lausanne
12 SIB - Swiss Institute of Bioinformatics [Lausanne]
13 LPGP - Laboratoire de Physiologie et Génomique des Poissons = Fish Physiology and Genomics Institute
14 GeT-PlaGe - Génome et Transcriptome - Plateforme Génomique
15 Nicholls State University
16 UNC - University of North Carolina [Charlotte]
2 HMS - Harvard Medical School [Boston]
3 Boston Children's Hospital
4 Harvard University
5 IBENS - Institut de biologie de l'ENS Paris
6 NC State - North Carolina State University [Raleigh]
7 SOKENDAI - Graduate University for Advanced Studies [Hayama]
8 Penn State - Pennsylvania State University
9 Cornell University [New York]
10 UC Davis - University of California [Davis]
11 UNIL - Université de Lausanne = University of Lausanne
12 SIB - Swiss Institute of Bioinformatics [Lausanne]
13 LPGP - Laboratoire de Physiologie et Génomique des Poissons = Fish Physiology and Genomics Institute
14 GeT-PlaGe - Génome et Transcriptome - Plateforme Génomique
15 Nicholls State University
16 UNC - University of North Carolina [Charlotte]
Elise Parey
- Fonction : Auteur
- PersonId : 744708
- IdHAL : elise-parey
- ORCID : 0000-0003-3394-2697
Tatsuya Ota
- Fonction : Auteur
- PersonId : 784024
- ORCID : 0000-0002-1115-5169
Kazuhiko Kawasaki
- Fonction : Auteur
- PersonId : 784022
- ORCID : 0000-0003-1090-5340
Mauricio Losilla
- Fonction : Auteur
- PersonId : 808562
- ORCID : 0000-0003-0695-3120
Qiaowei Pan
- Fonction : Auteur
- PersonId : 796950
- ORCID : 0000-0002-8501-0405
Romain Feron
- Fonction : Auteur
- PersonId : 743755
- IdHAL : romainferon
- ORCID : 0000-0001-5893-6184
Alexandra Louis
- Fonction : Auteur
- PersonId : 748563
- IdHAL : alexandra-louis
- ORCID : 0000-0001-7032-5650
- IdRef : 067130488
Jérôme Montfort
- Fonction : Auteur
- PersonId : 739749
- IdHAL : jerome-montfort
Yann Guiguen
- Fonction : Auteur
- PersonId : 739883
- IdHAL : yann-guiguen
- ORCID : 0000-0001-5464-6219
- IdRef : 094996423
Hugues Roest Crollius
- Fonction : Auteur
- PersonId : 175223
- IdHAL : hugues-roest-crollius
- ORCID : 0000-0002-8209-173X
- IdRef : 134614461
Camille Berthelot
- Fonction : Auteur
- PersonId : 763239
- ORCID : 0000-0001-5054-2690
- IdRef : 164058737
Ingo Braasch
- Fonction : Auteur
- PersonId : 801195
- ORCID : 0000-0003-4766-611X
Résumé
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.