Stylophora pistillata cell atlas illuminates stony coral symbiosis, calcification and immunity
Description
Stony corals are colonial cnidarians that sustain the most biodiverse marine ecosystems on Earth: coral reefs. Despite their ecological importance, little is known about the cell types and molecular pathways that underpin the biology of reef-building corals. Using single-cell RNA sequencing, here we define over 40 cell types across the life cycle of Stylophora pistillata. We discover specialized immune cells, and we uncover the developmental gene expression dynamics of calcium-carbonate skeleton formation. By simultaneously measuring the transcriptomes of coral cells and the algae within them, we characterize the metabolic programs involved in symbiosis in both partners. We also trace the evolution of these coral cell specializations by phylogenetic integration of multiple cnidarian cell type atlases. Overall, this study reveals the molecular and cellular basis of stony coral biology.
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This repository contains processed gene expression and annotation tables associated to the manuscript "Stylophora pistillata cell atlas illuminates stony coral symbiosis, calcification and immunity" Species acronyms: Spis -> Stylophora pistillata (this study) Xesp -> Xenia sp. (10.1038/s41586-020-2385-7) Nvec -> Nematostella vectensis (10.1016/j.cell.2018.05.019) Hvul -> Hydra vulgaris (10.1126/science.aav9314) For each species, the following files are included: *_broad_cell_type_gene_FC.tsv.gz -> Broad cell types normalized gene expression matrix (genes x broad cell types) *_cell_type_gene_FC.tsv.gz -> Cell types normalized gene expression matrix. *_metacell_gene_FC.tsv.gz -> Metacells normalized gene expression matrix. *_sc_UMI_counts.RDS -> Single-cell UMI counts matrix (genes x cells) *_gene_annotation.tsv.gz -> Gene annotation (Pfam domain architecture + Blast) *_transcription_factors.tsv.gz -> Phylogeny-based TF annotation. For Stylophora, single-cell ID to cell_type/metacell classification is provided for each stage: *_sc_cell_type_assignments *_sc_metacell_assignments In addition, we include: - the orthologous pairs generated with Broccoli (doi.org/10.1093/molbev/msaa159): orthologous_pairs.txt.gz - Stylophora Gene Ontology generated with EggNOG: Spis_Gene_Ontology.txt.gz - Stylophora gene intervals used for scRNA-seq quantification: Spis_mars_gene_intervals.txt.gz - Stylophora proteins used in this study: Spis_proteins.fasta.gz - Symbiodinium microadriaticum gene annotation: Smic_gene_annotation.txt.gz - Symbiodinium microadriaticum gene intervals used for scRNA-seq quantification: Smic_mars_gene_intervals.txt.gz - Symbiodinium microadriaticum proteins used in this study: Smic_proteins.fasta.gz