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Abstract
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DNA methylation is found throughout all domains of life, yet the extent and function of DNA
methylation differ among eukaryotes. Strains of the plant pathogenic fungus Zymoseptoria
tritici appeared to lack cytosine DNA methylation (5mC) because gene amplification followed
by Repeat-Induced Point mutation (RIP) resulted in the inactivation of the dim2 DNA
methyltransferase gene. 5mC is, however, present in closely related sister species. We
demonstrate that inactivation of dim2 occurred recently as some Z. tritici isolates carry a
functional dim2 gene. Moreover, we show that dim2 inactivation occurred by a different path
than previously hypothesized. We mapped the genome-wide distribution of 5mC in strains
with or without functional dim2 alleles. Presence of functional dim2 correlates with high levels
of 5mC in transposable elements (TEs), suggesting a role in genome defense. We identified
low levels of 5mC in strains carrying non-functional dim2 alleles, suggesting that 5mC is
maintained over time, presumably by an active Dnmt5 DNA methyltransferase. Integration
of a functional dim2 allele in strains with mutated dim2 restored normal 5mC levels, demonstrating
de novo cytosine methylation activity of Dim2. To assess the importance of 5mC for
genome evolution, we performed an evolution experiment, comparing genomes of strains
with high levels of 5mC to genomes of strains lacking functional dim2. We found that presence
of a functional dim2 allele alters nucleotide composition by promoting C to T transitions
(C!T) specifically at CpA (CA) sites during mitosis, likely contributing to TE inactivation.
Our results show that 5mC density at TEs is a polymorphic trait in Z. tritici populations that
can impact genome evolution.
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