The DNA methylation level against the background of the genome size and t-heterochromatin content in some species of the genus Secale L

Abstract

Methylation of cytosine in DNA is one of the most important epigenetic modifications in eukaryotes and plays a crucial role in the regulation of gene activity and the maintenance of genomic integrity. DNA methylation and other epigenetic mechanisms affect the development, differentiation or the response of plants to biotic and abiotic stress. This study compared the level of methylation of cytosines on a global (ELISA) and genomic scale (MSAP) between the species of the genus Secale. We analyzed whether the interspecific variation of cytosine methylation was associated with the size of the genome (C-value) and the content of telomeric heterochromatin. MSAP analysis showed that S. sylvestre was the most distinct species among the studied rye taxa; however, the results clearly indicated that these differences were not statistically significant. The total methylation level of the studied loci was very similar in all taxa and ranged from 60% in S. strictum ssp. africanum to 66% in S. cereale ssp. segetale, which confirmed the lack of significant differences in the sequence methylation pattern between the pairs of rye taxa. The level of global cytosine methylation in the DNA was not significantly associated with the content of t-heterochromatin and did not overlap with the existing taxonomic rye relationships. The highest content of 5-methylcytosine was found in S. cereale ssp. segetale (83%), while very low in S. strictum ssp. strictum (53%), which was significantly different from the methylation state of all taxa, except for S. sylvestre. The other studied taxa of rye had a similar level of methylated cytosine ranging from 66.42% (S. vavilovii) to 74.41% in (S. cereale ssp. afghanicum). The results obtained in this study are evidence that the percentage of methylated cytosine cannot be inferred solely based on the genome size or t-heterochromatin. This is a significantly more complex issue.

Keywords: ELISA; Genome size; MSAP; Methylation DNA; Secale; t-heterochromatin.

Figure 1. Methylation level (%) of Methylation-Susceptible Loci (MSL) in Secale taxons.

Type 1–unmethylated, type 2–internal cytosine methylation, type 3–hemimethylated, type 4–full methylation.

Figure 2. Principal Coordinate Analyses for epigenetic differentiation between the groups and Neighbor-Joining tree for epigenetic distances.

Principal Coordinate Analyses (PCoA) for epigenetic (MSL) differentiation between Secale taxons (A) and Secale species (B); (C): Neighbor-Joining tree of Secale species for epigenetic (MSL) distances; colors represent different taxons/species; (A), (B): C1 and C2 coordinates are shown with the percentage of variance explained by them, in (B) different point types represent subspecies from different species, species labels show the centroid for the points cloud in each species, ellipses represent the average dispersion of those points around their center, the long axis of the ellipse shows the direction of maximum dispersion and the short axis, the direction of minimum dispersion; cereale: S. cereale, S. c. ssp. afghanicum, S. c. ssp. segetale; strictum: S. strictum, S. s.ssp. africanum, S. s. ssp. kuprijanovii; sylvestre: S. sylvestre; vavilovii: S. vavilovii.

Figure 3. UPGMA dendrogram representing epigenetic relationships among rye taxons based on the data from MSAP analysis.

The numbers represent bootstrapping values.

Figure 4. The comparison of t-heterochromatin content and cytosine methylation.

Total telomeric heterochromatin content (%) in rye genomes, level (%) of cytosine methylation at CCGG sites from MSAP analysis, and global cytosine methylation (%) from ELISA analysis.

Figure 5. C-banded methaphase chromosomes of Secale, (A) Secale vavilovii, (B) Secale sylvestre.

Figure 6. 2C DNA nuclear content (pg).

* The 2C value for Secale cereale was used as reference value.