Yellow boxfish Ostracion cubicus embodies an evolutionary balance between conserved genomes and coral reef adaptations

Yellow boxfish Ostracion cubicus possesses specialized phenotypes adapted to coral reefs while retaining ancestral fused dermal plates. The contradictory evolutionary evidence hinders determining the true classification of O. cubicus. We constructed a more contiguous chromosome-level O. cubicus genome. The O. cubicus possessed the largest genome within the order Tetraodontiformes, which was primarily attributed to the amplification of transposable elements. Phylogenetic relationships based on 19 whole genomes and 131 mitochondrial genomes supported the division of Tetraodontiformes into three major sister groups (Ostraciontide-Molidae, Tetraodontidae, and Balistidae-Monacanthidae). Comparative genomic analyses supported that O. cubicus is a species close to the Tetraodontiformes ancestor, with the earlier divergence time and the most HOX gene family members. Despite overall genome conservation, some genetic and environmental changes may be key drivers of O. cubicus phenotypic adaptations, including climate cooling during Miocene-Pliocene Transition, recent DNA and LINE transposon bursts, unique chromosomal rearrangements, and gene family expansion. Many positive selection genes and rapidly evolving genes were associated with skeletal development, such as bmp7, egf7, and bmpr2. Besides, comparative transcriptome analysis between O. cubicus carapace and tail skin revealed various candidate genes and pathways related to carapace formation, such as postn, scpp1, and TGF-β cytokines signaling. One eda amino acid mutation and protein structure prediction may indicate convergent evolution of teleost bony plates. Our study provides new insights into dermal carapace evolution and how boxfish adapt to coral reefs, offering a strong case for evolutionary balance between conserved genome and non-conserved factors driving coral reef adaptation in Ostracion cubicus.