Polyploidy drives DNA methylation patterns and gene expression variability differences in Pocillopora acuta

Strand, E.L.1,2*, Stephens, T.3, Chille, E.3, Wong, K.1,4, Bhattacharya, D.3, Putnam, H.M.1

1 Department of Biological Sciences, University of Rhode Island, Kingston, Rhode Island, USA
2 Gloucester Marine Genomics Institute, Gloucester, Massachusetts, USA
3 Department of Biochemistry and Microbiology, Rutgers, The State University of New Jersey, New Brunswick, New Jersey, USA
4 Department of Marine Biology and Ecology, University of Miami Rosenstiel School of Marine and Atmospheric Science, Miami, Florida, USA

Figure 1. Experimental design for P. acuta molecular analyses. A) Field collection sites in Kāneʻohe Bay, Oʻahu, Hawaiʻi. Six sites were sampled including Lilipuna dock, HIMB, Reef 18, Reef 11.13, Reef 35.36, and Reef 42.43. B) Image of study species, Pocillopora acuta. C) Color score results of the molecular samples over the course of the exposure period (week 2-8) and in recovery (week 12). The dotted line indicates when stress treatments were turned off (Strand et al., 2024). D) Gene expression results that support a genotype and polyploidy driven expression pattern from Chille et al., 2024.

Figure 2. Fig 2. A,B) PCA of mean CpG loci % methylation per gene for all genes with data for >5 CpG positions (n=9,467 genes). A) PCA overlaid with time point and treatment. B) PCA overlaid with polyploidy group defined by Stephens et al., 2023 and Chille et al., 2024. C) Mean CpG loci % methylation per gene for all significantly differentially methylated genes with median >10% methylation (n=1,796 genes). Each point represents a coral sample. D) Heatmap of z-scores of mean CpG loci % methylation for significantly differentially methylated genes (DMGs; n=1,447 genes) by individual coral samples from methylation pattern groups: Diploidy (D; n=15 corals), Triploidy 1 (T1; n=20 corals), and Triploidy 2 (T2; n=16 corals). Z-scores calculated by subtracting the mean and then dividing by the standard deviation for each gene. Color indicates ploidy groups.