Deciphering omics atlases to aid stony corals in response to global change

Coral reefs are rapidly declining due to global climate change ¹ . Alongside environmental protection, gene engineering technologies are essential in protecting reef-building (stony) corals ^2-7 . Precise multi-omics backgrounds are crucial for gene technique application ^8-13 and understanding stony coral biology ^2-5 . However, high heterozygosity ^4,14 and exogenous sequence contamination ^15-17 impede high-quality stony coral genome assembly. To address this, we developed a workflow for stony coral genome assembly, achieving four high-quality chromosome-level genomes ( Acropora muricata , Montipora foliosa , M. capricornis , and Pocillopora verrucosa ). A global synteny analysis of chromosomes and homeobox genes highlighted the highly conserved features of Scleractinia stony coral genomes, even after an evolutionary divergence 250 million years ago (mya). Single-cell RNA sequencing (scRNA-seq), combined with a pan-genomic analysis, aided our understanding of symbiosis and calcification, both issues of conservation concern. A dynamics simulation of the mechanism of systemic RNA interference defective protein 1 transmembrane family member 1 (SIDT1) tetramer offered a potential approach to observe gene impacts on stony corals. This work enhances understanding of the evolutionary, molecular, and cellular aspects of stony corals and provides a detailed dataset for applying gene engineering technologies in response to global climate challenges.