Patterns of repeat-induced point mutation in transposable elements of basidiomycete fungi

Abstract

Transposable elements (TEs) are ubiquitous genomic parasites that have prompted the evolution of genome defense systems that restrict their activity. Repeat-induced point mutation (RIP) is a homology-dependent genome defense that introduces C-to-T transition mutations in duplicated DNA sequences and is thought to control the proliferation of selfish repetitive DNA. Here, we determine the taxonomic distribution of hypermutation patterns indicative of RIP among basidiomycetes. We quantify C-to-T transition mutations in particular di- and trinucleotide target sites for TE-like sequences from nine fungal genomes. We find evidence of RIP-like patterns of hypermutation at TpCpG trinucleotide sites in repetitive sequences from all species of the Pucciniomycotina subphylum of the Basidiomycota, Microbotryum lychnidis-dioicae, Puccinia graminis, Melampsora laricis-populina, and Rhodotorula graminis. In contrast, we do not find evidence for RIP-like hypermutation in four species of the Agaricomycotina and Ustilaginomycotina subphyla of the Basidiomycota. Our results suggest that a RIP-like process and the specific nucleotide context for mutations are conserved within the Pucciniomycotina subphylum. These findings imply that coevolutionary interactions between TEs and a hypermutating genome defense are stable over long evolutionary timescales.

FIG. 1.—

Proportion of various dinucleotide sequences with C-to-T mutations in two alignments of TE-like repeat sequences from the ascomycete fungus Neurospora crassa. Numbers and lengths of aligned sequences are given in table 2. Overall mutation rate μ of each alignment was calculated as the total number of mutations relative to the consensus sequence divided by the total number of base pairs in the alignment. Mutation rates of cytosine residues in particular sequence contexts are shown as the proportion of dinucleotide combinations in the consensus sequence with C-to-T mutation frequency among sequences in the alignment exceeding the threshold defined by the mutation rate μ for that particular alignment, as described in the text. Standard International Union of Biochemistry (IUB) codes are used for incompletely specified nucleotides: B indicates nucleotides other than A. Bars represent the 95% confidence intervals associated with the proportion of nucleotide combinations with mutation frequency among sequences exceeding the mutation threshold.

Fig. 2.—

Proportion of various trinucleotide sequences with C-to-T mutations in representative alignments of TE-like repeat sequences from species of the fungal basidiomycete subphylum Pucciniomycotina. Alignment of TE-like sequences from Microbotryum lychnidis-dioicae is composed of 9 sequences of a Copia-like element; Puccinia graminis, 10 sequences of a Gypsy-like element; Melampsora laricis-populina, 21 sequences of a Gypsy-like element; Rhodotorula graminis, 65 sequences of a Gypsy-like element; analysis of other alignments is presented in table 2. Overall mutation rate μ of each alignment was calculated as the total number of mutations relative to the consensus sequence divided by the total number of base pairs in the alignment. Mutation rates of cytosine residues in particular sequence contexts are shown as the proportion of trinucleotide combinations in the consensus sequence with C-to-T mutation frequency among sequences in the alignment exceeding the threshold defined by the mutation rate μ for that particular alignment, as described in the text. Standard IUB codes are used for incompletely specified nucleotides: V indicates nucleotides other than T; H indicates nucleotides other than G. Bars represent the 95% confidence intervals associated with the proportion of nucleotide combinations with mutation frequency among sequences exceeding the mutation threshold.

Fig. 3.—

Molecular phylogenetic analysis of the taxa used in the analysis based on the partial sequence of the 18S ribosomal RNA gene. The evolutionary history was inferred by using the maximum likelihood method based on the Kimura 2-parameter model (Kimura 1980). The percentage of replicate trees in which the associated taxa clustered together in the bootstrap test (1,000 replicates) are shown next to the branches (Felsenstein 1985). Branches corresponding to partitions reproduced in less than 50% bootstrap replicates are collapsed. The tree is drawn to scale, with branch lengths measured in the number of substitutions per site. The analysis involved nine nucleotide sequences. There were a total of 1367 positions in the final data set. Evolutionary analyses were conducted in MEGA5 (Tamura et al. 2011). Hypermutation patterns detected in this study are indicated below the branch at the base of the clade in which the pattern is found in all taxa examined.