Yellow boxfish Ostracion cubicus genome evolution

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.O. cubicus genome and all raw sequence data reported (RNA-seq, Hi-C, PacBio WGS, and Illumina WGS) have been deposited in this submission.