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

Abstract

Coral reefs are rapidly declining due to global climate change1. Alongside environmental protection, gene engineering technologies are essential in protecting reef-building (stony) corals2-7. Precise multi-omics backgrounds are crucial for gene technique application8-13 and understanding stony coral biology2-5. However, high heterozygosity4,14 and exogenous sequence contamination15-17 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.