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.

Coral transcriptomic data largely rely on short-read sequencing, which severely limits the understanding of coral molecular mechanisms and leaves many important biological questions unresolved. Here, we sequence the full-length transcriptomes of four common and frequently dominant reef-building corals using the PacBio Sequel II platform. We obtain information on reported gene functions, structures, and expression profiles. Among them, a comparative analysis of biomineralization-related genes provides insights into the molecular basis of coral skeletal density. The gene expression profiles of the symbiont Symbiodiniaceae are also isolated and annotated from the holobiont sequence data. Finally, a phylogenetic analysis of key circadian clock genes among 40 evolutionarily representative species indicates that there are four key members in early metazoans, including cry genes; Clock or Npas2; cyc or Arntl; and tim, while per, as the fifth member, occurs in Bilateria. In summary, this work provides a foundation for further work on the manipulation of skeleton production or symbiosis to promote the survival of these important organisms.

Background: Reef-building corals are critical species for sustaining coral reefs and are highly threatened by global climate change. However, relevant transcriptomic data largely rely on short-read sequencing, which severely limits the understanding of coral molecular mechanisms and leaves many important biological questions unresolved. Results: We sequenced the full-length transcriptomes of four common and frequently dominant reef-building corals, including two Robusta clade species, Pocillopora damicornis and Pocillopora verrucosa , and two Complexa clade species, Acropora muricata and Montipora foliosa, using the PacBio Sequel II platform. We obtained information on gene functions, structures and expression profiles. Among them, a comparative analysis of biomineralization-related genes provided insights into the molecular basis of coral skeletal density. The gene expression profiles of the symbiote Symbiodiniaceae were also isolated and annotated from the holobiont sequence data; these profiles showed more highly convergent traits related to gene structure and expression level than those of coral hosts. Interestingly, we observed that intracellular algal cells share some evolutionary convergence between intracellular symbiosis in corals and intracellular digestion in amphioxus. Finally, a phylogenetic analysis of key circadian clock genes among 27 evolutionarily representative species indicated that there are four key members in early metazoans, including cry genes; Clock or Npas2 ; cyc or Arntl ; and tim , while per , as the fifth member, occurs in Bilateria. Conclusions: Our work overcomes the incompleteness of short-read sequencing and illuminates the molecular basis of calcification, symbiosis, and circadian genes, thus providing a foundation for further work on the manipulation of skeleton production or symbiosis to promote the survival of these important organisms.

The coral reef ecosystem faces increasing threats under global climate challenges. One of the core issues is the inability of fragments to quickly grow into a size that can resist environmental pressures in coral transplantation. The observation of accelerated growth during the early stages of coral regeneration provides new insights for addressing this challenge. To investigate related molecular mechanisms, our study focused on the fast-growing stony coral Acropora muricata (with chromosome-scale reference genome). Employing diverse techniques, including single-cell RNA sequencing (scRNA-seq), we unveiled related intricate cellular dynamics. Single-cell analysis revealed notable shifts in calicoblasts and epidermal cells around 2-4 weeks post-injury. Gene expression analysis revealed enrichment in immune response and biomineralization pathways. Pseudotime analysis explained the differentiation of epidermal cells into calicoblasts, while time-course analysis identified key genes associated with dynamic biomineralization changes. This study enhances our understanding of coral regeneration, offering insights for protective strategies to foster coral growth.

During early mammalian embryogenesis, totipotent zygotes and early blastomeres undergo extensive post‐transcriptional regulation during the establishment of the first cell lineages; however, the functional contribution of alternative splicing to embryonic compaction and blastulation remains poorly understood. Here, we show that SF3B1, a core component of the spliceosome, is upregulated from the 4‐cell stage and mediates highly dynamic splicing programs. Depletion of SF3B1 results in developmental arrest at the morula stage, accompanied by widespread transcriptomic dysregulation characterized by aberrant expression of transcription factors that impede pluripotency transition. Alternative splicing analysis further identifies that aberrantly spliced transcripts were significantly enriched in genes involved in cell cycle regulation, such as Cdk11b and Ccnb1 . Importantly, we demonstrate that SF3B1 undergoes intrinsic, IDR‐driven liquid‐liquid phase separation both in vitro and in vivo, forming nuclear condensates in oocytes and early embryos, which is essential for successful development to the blastocyst stage. Together, our findings reveal that phase separation mediated SF3B1 splicing activity is a critical regulator of early mouse embryonic development.

Liquid-liquid phase separation (LLPS) regulates protein function by organizing proteins into dynamic condensates, yet how divergence in LLPS among orthologs gives rise to species-specific functional outputs remains poorly understood. Here, we show that intrinsically disordered regions (IDRs) act as transferable modules whose sequence composition encodes phase separation capacity and functional outputs. Incorporating the QPGY domain from human SS18 into its yeast ortholog Snf11 yields a chimeric protein (Snf11-QPGY) that forms dynamic intracellular condensates. These condensates activate the adhesion genes FLO1 and FLO11, triggering calcium-dependent flocculation absent in wild-type cells. Mechanistically, Snf11-QPGY sequesters histone deacetylase subunit Rpd3 within condensates, reducing its occupancy at FLO promoters and promoting histone acetylation and transcriptional activation. Substituting QPGY with a heterologous LLPS-competent IDR restores condensate formation but does not recapitulate QPGY-driven transcriptional-phenotypic outputs. These findings reveal how evolutionary diversification of IDR sequences drives functional divergence among orthologs and offer a framework for engineering IDR-dependent regulatory modules.