Hidden diversity and host specificity of Cladocopium symbionts revealed by phylotranscriptomics in giant sea anemones.

Hidden diversity and host specificity among Symbiodiniaceae symbionts in giant sea anemones have been uncovered through the use of phylotranscriptomics. These symbionts, which form a close, metabolically linked relationship with the anemones, have proven to be poorly characterized despite the well-documented association with anemonefish.

Using RNA-sequencing and advanced phylogenetic approaches, researchers identified distinct Symbiodiniaceae strains in seven different sea anemone species, as well as four cryptic lineages of Entacmaea quadricolor. Traditional molecular markers, such as the Internal Transcribed Spacer 2 (ITS2) or partial 28S ribosomal DNA, were found to be less sensitive in resolving relationships among these symbionts compared to transcriptome-wide phylogenetic methods.

The phylogenies of 1300 and 214 nuclear genes revealed that these Symbiodiniaceae strains are novel and specific to their respective sea anemone hosts, with clustering patterns indicating a nonrandom association between host and symbiont evolutionary histories. Two previously identified cryptic lineages of E. quadricolor harbor distinct Symbiodiniaceae assemblages, with significant functional divergence detected between these symbiont strains.

Three-dimensional reconstructions of the symbiont cells using serial block-face scanning electron microscopy further support their unique cellular organization and functional identity. These findings reveal a previously unrecognized level of diversity within the Symbiodiniaceae algal symbionts of giant sea anemones, suggesting that the evolutionary history of these algal partners mirrors the diversification of their host species in this tripartite symbiosis.