Within-colony color variation in a chalice coral is associated with region-specific pigment expression and higher photoconvertible pigment transcripts

A single colony of colonial coral often exhibits noticeable color variation, but the molecular basis of this within-colony variation remains unclear. Despite originating from the same genetic background, tissues within a single colony show distinct colors, suggesting that differences arise from regulatory mechanisms rather than genetic ones.

This pilot study sought to investigate the transcriptional mechanisms underlying color regions in a green-and-orange chalice coral colony through a comprehensive transcriptomic analysis. Researchers collected samples from three areas: the green body, the orange oral region, and a transition region between them. The resulting holobiont transcriptome was assembled de novo from RNA-seq data, with coral host transcripts differentiated from those of the dinoflagellate symbiont.

The green fluorescent protein (GFP)-like pigment genes were classified phylogenetically, and their expression quantified using host-only normalization to account for regional differences in symbiont read fraction. Compared to the green body, the orange oral region displayed higher expression of two sets of host pigment genes: distinct orange fluorescent-protein and chromoprotein transcripts, as well as green-to-red photoconvertible EosFP-family proteins, whose unconverted form is green.

This study demonstrates that different color regions within a single colony are associated with region-specific upregulation of various pigment transcripts, including both directly colored proteins and those capable of photoconversion. Further research is required to confirm whether photoconversion indeed contributes to the coloration and to determine if this pattern is consistent across multiple colonies.