Genomic CG dinucleotide deficiencies associated with transposable element hypermutation in Basidiomycetes, some lower fungi, a moss and a clubmoss

- Dinucleotide scans reveal CG deficient fractions in Basidiomycete and other genomes.
- Many transposable elements exhibit extensive CG to TG hypermutation.
- CG and CHG deficiencies in two lower plants link hypermutation to methylation.
- CG hypermutation also affects gene families, but has not prevented their expansion.
- Limited CG deficiency in many fungi implies other mechanisms for control of repeats.

Many Basidiomycete genomes include substantial fractions that are deficient in CG dinucleotides, in extreme cases amounting to 70% of the genome. CG deficiency is variable and correlates with genome size and, more closely, with transposable element (TE) content. Many species have limited CG deficiency; it is therefore likely that there are other mechanisms that can control TE proliferation. Examination of TEs confirms that C-to-T transition mutations in CG dinucleotides may comprise a conspicuous proportion of differences between paired elements, however transition/transversion ratios are never as high as those due to RIP in some Ascomycetes, suggesting that repeat-associated CG mutation is not totally pervasive. This has allowed gene family expansion in Basidiomycetes, although CG transition differences are often prominent in paired gene family members, and are evidently responsible for destruction of some copies. A few lower fungal genomes exhibit similar evidence of repeat-associated CG mutation, as do the genomes of the two lower plants Physcomitrella patens and Selaginella moellendorffii, in both of which mutation parallels published methylation of CHG as well as CG nucleotides. In Basidiomycete DNA methylation has been reported to be largely confined to CG dinucleotides in repetitive DNA, but while methylation and mutation are evidently associated, it is not clear which is cause and which effect.

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