Stony corals preserve the most conserved Precambrian core in animals

<title>Abstract</title> <p>Scleractinian corals owe their ecological success to long-enigmatic genomic innovations. By reconstructing ancestral linkage groups (ALGs) across 222 high-quality chromosome-level metazoan genomes at key evolutionary nodes spanning the bilaterian–cnidarian–sponge lineage, we propose the concepts of Precambrian “proto-cell type” and post-Cambrian “derived cell type” based on ALG–chromosome correspondence, showing that scleractinian corals represent a typical proto-cell type by preserving the most conserved Precambrian chromosomal core. From the ancestral 28-chromosome karyotype, they evolved a stable 14-chromosome architecture through progressive fusions while maintaining intact synteny for over 450 million years—the greatest such conservation in animals. This stability enabled coupled evolution of endosymbiosis and biomineralization, as revealed by pan-genomic single-cell transcriptomic analyses. These findings illuminate metazoan karyotype evolution and inform coral reef conservation.</p>