Evolutionary balance between genomic conservation and coral reef adaptation in the yellow boxfish ( Ostracion cubicus).

The yellow boxfish ( Ostracion cubicus) exhibits a combination of derived morphological traits specialized for coral reef environments and ancestral characteristics, including a fused dermal plate. Contradictory evolutionary evidence hinders true classification of O. cubicus. To clarify its evolutionary position within Tetraodontiformes, a chromosome-level genome assembly was generated, representing the most contiguous and complete genome to date for this lineage. Notably, O. cubicus possessed the largest genome within the order Tetraodontiformes, primarily due to extensive transposable element expansion. Phylogenetic analysis based on 19 whole genomes and 131 mitochondrial genomes resolved Tetraodontiformes into three major sister groups (Ostraciidae-Molidae, Tetraodontidae, and Balistidae-Monacanthidae). Comparative genomic evidence indicated that O. cubicus diverged early from the common ancestor of modern Tetraodontiformes and retained the highest number of HOX genes among surveyed taxa. Although overall genomic architecture was largely conserved, certain genetic and environmental changes may have contributed to its phenotypic adaptations, including climate cooling during the Miocene-Pliocene Transition, recent DNA and long interspersed nuclear element (LINE) transposon bursts, lineage-specific chromosomal rearrangements, and gene family expansion. Many positively selected genes and rapidly evolving genes were associated with skeletal development, including bmp7, egf7, and bmpr2. Transcriptomic comparisons between carapace and tail skin revealed various candidate genes and pathways related to carapace formation, such as postn, scpp1, and components of the TGF-β signaling pathway. A derived amino acid substitution in eda, coupled with protein structural modeling, suggested potential molecular convergence in dermal plate formation among teleosts. These findings provide novel insights into the genomic and developmental basis of carapace evolution and coral reef-adaptation in O. cubicus, offering a strong case for evolutionary balance between genomic conservation with regulatory innovation to achieve coral reef specialization.