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Abstract The cell type-specific expression of key transcription factors is central to development and disease.Brachyury/T/TBXTis a major transcription factor for gastrulation, tailbud patterning, and notochord formation; however, how its expression is controlled in the mammalian notochord has remained elusive. Here, we identify the complement of notochord-specific enhancers in the mammalianBrachyury/T/TBXTgene. Using transgenic assays in zebrafish, axolotl, and mouse, we discover three conservedBrachyury-controlling notochord enhancers,T3,C, andI, in human, mouse, and marsupial genomes. Acting as Brachyury-responsive, auto-regulatory shadow enhancers,in cisdeletion of all three enhancers in mouse abolishes Brachyury/T/Tbxt expression selectively in the notochord, causing specific trunk and neural tube defects without gastrulation or tailbud defects. The threeBrachyury-driving notochord enhancers are conserved beyond mammals in thebrachyury/tbxtbloci of fishes, dating their origin to the last common ancestor of jawed vertebrates. Our data define the vertebrate enhancers forBrachyury/T/TBXTBnotochord expression through an auto-regulatory mechanism that conveys robustness and adaptability as ancient basis for axis development. 

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.