High-contiguity temperate coral genome reveals thematic gene enrichment and assembly quality effects in comparative genomics

Abstract Reef-building Acropora corals face climate change threats, necessitating genomic resources to understand adaptation, particularly at range edges. Temperate populations of Acropora hyacinthus , like those in Kochi, Japan, are genetically distinct but lack a high-quality reference genome, hindering comparative studies. We generated a 480.16 Mb, highly contiguous (N50 6.99 Mb) PacBio HiFi genome assembly for Kochi A. hyacinthus , achieving 94.0% BUSCO completeness. Phylogenomic analysis using 588 single-copy orthologs confirmed significant divergence between the Kochi and subtropical Okinawa populations, placing Kochi within Acropora Clade IV but on a distinct, longer branch. The enhanced contiguity resolved complex genomic regions; notably, we identified and characterized two distinct, co-localized FOX gene paralogs (AhyaKCZ.442 and the divergent AhyaKCZ.437) within an orthogroup (OG0009671) significantly expanded in Kochi (Z = 3.881) and typically containing a single copy in other Acropora . The divergent paralog (AhyaKCZ.437) exhibits unique structural features, including an ammonium transporter motif, and a basal phylogenetic position, suggesting potential functional novelty relevant to temperate adaptation. While comparative analysis revealed substantial gene count differences in expanded orthogroups relative to a short-read reference (e.g., 21.89 vs 2.445 mean genes), methodological differences in sequencing and assembly likely contribute significantly to this disparity. This first high-quality temperate A. hyacinthus genome provides a critical resource for investigating regional adaptation, demonstrates the power of long-read sequencing for resolving paralogs, and underscores the need for comparable datasets in comparative genomics.