Distribution of methylcytosine in plant genomes

Plant genomes are dynamic and differ strongly in size due to differences in gene content, the number of transposons, or other repetitive sequences, which influence the diversification of DNA methylation mechanisms (Chad E. & Schmitz, 2017; Pellicer, Hidalgo, Dodsworth, & Leitch, 2018). Several genome-wide methylome studies applying bisulfite sequencing (BiSeq) (see Chapter 11) demonstrated that plants have a higher epigenome diversity among species than animals (Fig. 6). This can be attributed to genetic variation, for example, large differences in the amount of heterochromatin and to the three different cytosine contexts in plants (Jones, 2012; Niederhuth et al., 2016; Pellicer et al., 2018; Yi, 2017).

Early papers reported cytosine methylation is mainly restricted to the nuclear DNA, suggesting DNA methylation in plastid genomes does not play a role in controlling gene activity (Ahlert, Stegemann, Kahlau, Ruf, & Bock, 2009; Finnegan, Genger, Peacock, & Dennis, 1998). However, high levels of N6-methyladenosine (m6A) methylation findings in the chloroplast and mitochondria propose the presence of methylation machinery inside these organelles. In addition, RNA methylation was identified, although its role in plant organelles is yet not fully understood (Manduzio & Kang, 2021).

The distribution of methylcytosines over the nuclear genome varies among species. Generally, it is concentrated in regions rich in repeated sequences, which include the centromere surrounding DNA and telomeres, or in genome regions containing many transposons (Finnegan, Genger, Peacock, & Dennis, 1998).

Such patterns of context-dependent accumulation of cytosine methylation can also be seen on a smaller scale. When we average methylation frequency across genes, transcription start sites, or transposons, as shown in the next infographic (Fig. 7).

The comparative epigenomic analysis identifies how dynamic the methylomes between flowering plant species can be. Families such as Brassicaceae and most Poaceae showed globally lower mCHG and mCHH methylation than other plants. One reason for these pronounced differences is that large genomes, like Zea mays, contain much higher numbers of repetitive sequences and transposons than smaller genomes, like strawberry. These sequences are commonly characterized by higher methylation levels. On the other hand, the gbM of ortholog genes showed a conserved pattern across species (Niederhuth et al., 2016). In conclusion, the variation in DNA methylation between plant species opens new areas of study to understand the role of DNA methylation and their correlation with evolutionary distance as well as biological diversity.