Single-cell transcriptome sequencing reveals the cell populations and functions associated with stony coral Pocillopora damicornis

Introduction Pocillopora damicornis , a key species of stony corals, has been the subject of considerable scientific study. However, the cellular composition of P. damicornis and the roles of these cells in endosymbiosis and biomineralization remain elusive. The development of single-cell technology has provided new opportunities for researching the cellular and molecular mechanisms underlying symbiosis and mineralization. Nevertheless, the stringent environmental requirements, the complexity of the cellular components, and the paucity of high-quality reference genomes of P. damicornis have posed significant challenges for single-cell transcriptome research. Methods In this study, we quantified the transcriptomic expression of P. damicornis by aligning its single-cell transcriptome (scRNA-seq) data to multiple species, including Stylophora pistillata , P. damicornis , and Pocillopora verrucosa . We determined the cell types of P. damicornis by comparing its cluster-specific genes with the published cell type-specific genes of S.pistillata and conducted gene function and enrichment analyses. Results Unsupervised clustering analysis yielded the identification of ten distinct cell populations, including epidermis cells, gastrodermis cells, algae-hosting cells, calicoblast, cnidocytes, and immune cells. In addition, we identified 53 genes that were highly similar to known sequences in the symbiotic zooxanthellae. These genes were mainly expressed in four different cell populations, corresponding to active symbiotic populations. Conclusion This study identified cell types closely associated with symbiosis and calcification in P. damicornis , along with their marker genes, which are consistent with the findings in S. pistillata . These results offer insights into the cellular functions and symbiotic mechanisms of P. damicornis .