In-depth single-cell transcriptomic exploration of the regenerative dynamics in stony coral

Abstract Coral reef ecosystems face escalating threats from anthropogenic global climate challenges, leading to frequent bleaching events. A key issue in coral transplantation is the inability of fragments to rapidly grow to sizes that can resist environmental pressures. The observation of accelerated growth during the early stages of coral regeneration provides new insights for addressing this challenge. To investigate the underlying molecular mechanisms, we study the fast-growing stony coral Acropora muricata. Using single-cell RNA sequencing, bulk RNA sequencing, and high-resolution micro-computed tomography, we identify a critical regeneration phase around 2–4 weeks post-injury. Single-cell transcriptome analysis reveals 11 function-specific cell clusters. Pseudotime analysis indicates epidermal cell differentiation into calicoblasts. Bulk RNA-seq results highlight a temporal limitation in coral’s rapid regeneration. Through integrated multi-omics analysis, this study emphasizes the importance of a comprehensive understanding of coral regeneration, providing insights beyond fundamental knowledge and offering potential protective strategies to promote coral growth.