Transcriptomes and expression profiling of deep-sea corals from the Red Sea provide insight into the biology of azooxanthellate corals

Abstract

Despite the importance of deep-sea corals, our current understanding of their ecology and evolution is limited due to difficulties in sampling and studying deep-sea environments. Moreover, a recent re-evaluation of habitat limitations has been suggested after characterization of deep-sea corals in the Red Sea, where they live at temperatures of above 20 °C at low oxygen concentrations. To gain further insight into the biology of deep-sea corals, we produced reference transcriptomes and studied gene expression of three deep-sea coral species from the Red Sea, i.e. Dendrophyllia sp., Eguchipsammia fistula, and Rhizotrochus typus. Our analyses suggest that deep-sea coral employ mitochondrial hypometabolism and anaerobic glycolysis to manage low oxygen conditions present in the Red Sea. Notably, we found expression of genes related to surface cilia motion that presumably enhance small particle transport rates in the oligotrophic deep-sea environment. This is the first study to characterize transcriptomes and in situ gene expression for deep-sea corals. Our work offers several mechanisms by which deep-sea corals might cope with the distinct environmental conditions present in the Red Sea As such, our data provide direction for future research and further insight to organismal response of deep-sea coral to environmental change and ocean warming.

Figure 1

Enrichment of Pfam-based protein domains of three deep-sea coral transcriptomes in comparison to genomic gene sets of other cnidarians. Rows depict Z-score transformed Pfam domain counts and columns represent organisms. Only significantly enriched domains in deep-sea corals are displayed (FDR < 0.05). Rows are clustered by Euclidean distance. Color key indicates domain counts over row z-scores alongside distribution (histogram). Dsp = Dendrophyllia sp., Efis = Eguchipsammia fistula, Rtyp = R. typus, Spis = Stylophora pistillata, Adig = Acropora digitifera, Aip = Aiptasia, Nvec = Nematostella vectensis, Hmag = Hydra magnipapillata.

Figure 2

Overview of selected enriched GO biological process terms for highly expressed genes (FPKM > 100). Values represent the number of shared and exclusive GO terms of three deep-sea coral species from the Red Sea.

Figure 3

Heatmap of 431 differentially expressed orthologous genes between Dendrophyllia sp., E. fistula, and R. typus. Colors denote log₂(x + 1) transformed FPKM values.