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

Reef-building Acropora corals face climate change threats, necessitating genomic resources to understand adaptation, particularly at range edges. Temperate lineages of Acropora hyacinthus in Kochi, Japan, are genetically distinct but lack a high-quality reference genome. We generated a 480.16 Mb, highly contiguous (contig N50 6.99 Mb) PacBio HiFi genome assembly for Kochi A. hyacinthus, achieving 94.0% BUSCO completeness. Phylogenomic analysis using 434 single-copy orthologs revealed a close sister relationship between the temperate Kochi and tropical Palau lineages, which were clearly distinct from the subtropical Okinawa lineage. Comparative analysis identified apparent enrichments in gene families linked to innate immunity (C-type lectins) and genome restructuring (transposable elements). This result highlights a key methodological difference: the high-contiguity assembly resolves complex, repetitive gene families that are likely undercounted in short-read reference genomes, meaning the observed expansions in this study reflect either potential biological divergence or higher technical resolution and needs further comparison with other hi-fi Acropora genomes in the future. Nevertheless, this first high-quality temperate A. hyacinthus genome provides a foundational resource for investigating regional adaptation and illustrates that the use of comparable, high-contiguity assemblies is essential for the accuracy of future comparative genomic studies.