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.

弓鳍鱼（ Amia calva ）是一种射线鳍鱼，拥有一套独特的祖先和衍生表型，这是了解脊椎动物进化的关键。弓鳍鱼作为新翅目鱼类代表的系统发育地位、其典型的身体结构及其不重复且缓慢进化的基因组使弓鳍鱼成为射线鳍鱼类基因组探索的中心物种。在这里，我们提出了弓鳍鱼的染色体水平基因组组装，可以进行基因顺序分析，解决了长期争论的新翅目系统发育关系。我们通过弓鳍发育检查染色质可及性和基因表达，以研究免疫、鳞片、呼吸和鳍骨骼系统的进化，并鉴定脊椎动物中数百个保守的基因调控位点。这些资源将硬骨鱼的发育进化联系起来，进一步凸显了弓鳍鱼对于阐明基因组时代脊椎动物生物学和多样性的重要性。