Chloroplast DNA methylation in the kelp Saccharina latissima is determined by origin and possibly influenced by cultivation

Abstract

DNA cytosine methylation is an important epigenetic mechanism in genomic DNA. In most land plants, it is absent in the chloroplast DNA. We detected methylation in the chloroplast DNA of the kelp Saccharina latissima, a non-model macroalgal species of high ecological and economic importance. Since the functional role of the chloroplast methylome is yet largely unknown, this fundamental research assessed the chloroplast DNA cytosine methylation in wild and laboratory raised kelp from different climatic origins (High-Arctic at 79° N, and temperate at 54° N), and in laboratory samples from these origins raised at different temperatures (5, 10 and 15°C). Results suggest genome-wide differences in methylated sites and methylation level between the origins, while rearing temperature had only weak effects on the chloroplast methylome. Our findings point at the importance of matching conditions to origin in restoration and cultivation processes to be valid even on plastid level.

Keywords: aquaculture; epigenetics; marine algae; marine macrophyte; non‐model organism; organelle genome methylation; plastid.

FIGURE 1

Differences in methylated sites and methylation level between conditions. Methylated CG sites (a, b), and methylation levels as reads per million (RPM) for CHG sites (c, d) between populations and temperatures in laboratory samples (a, c) and compared between origins (b, d). ns, Not significant. Numbers at the bottom of the bars indicate sample size. Significance codes after p‐value correction (Benjamini–Hochberg) for multiple comparisons: ‘<0.05’: *, ‘<0.01’: **, ‘<0.001’: ***, ‘<0.0001’: ****.

FIGURE 2

Principal component analysis for (a) Laboratory samples of both origins grouped by temperature treatment. (b) Laboratory samples grouped by origin. (c) All samples, grouped by origin. (d) Field samples grouped by origin. Ellipses represent 95% confidence intervals around the group medians.

FIGURE 3

VennEuler diagram showing the numbers of differentially methylated sites between Helgoland and Spitsbergen when analysing field samples (blue), and laboratory samples (orange; Tables S2 and S3). The labels give the product of the genes that were differentially methylated in the respective partitions. (_1) and (_2) depict a gene that showed differential methylation at two different sites. For the exact site position in the respective gene, see Table S6 (‘ST6 Origins’).

FIGURE 4

Epigenetic distances in the chloroplast and nuclear methylome (‘genome’). The corresponding mantel test showed that the chloroplast methylome did not in general mirror the nuclear methylome (r = 0.145).

FIGURE 5

Epigenetic distance (Euclidean distance) for ‘cultivation’, Laboratory (orange) and Field (blue) samples (a), and for ‘origin’, Helgoland (yellow) and Spitsbergen (green) samples (b). The small black dots depict the pairwise distances between the individual samples of each. The light grey dots are outliers detected by the boxplot script but were included during epi‐distance analyses. The boxes represent the interquartile range (IQR) of the respective group, and the horizontal line within the boxes gives the median Euclidean distance.