Genome-Wide Analyses of Repeat-Induced Point Mutations in the Ascomycota

Abstract

The Repeat-Induced Point (RIP) mutation pathway is a fungus-specific genome defense mechanism that mitigates the deleterious consequences of repeated genomic regions and transposable elements (TEs). RIP mutates targeted sequences by introducing cytosine to thymine transitions. We investigated the genome-wide occurrence and extent of RIP with a sliding-window approach. Using genome-wide RIP data and two sets of control groups, the association between RIP, TEs, and GC content were contrasted in organisms capable and incapable of RIP. Based on these data, we then set out to determine the extent and occurrence of RIP in 58 representatives of the Ascomycota. The findings were summarized by placing each of the fungi investigated in one of six categories based on the extent of genome-wide RIP. In silico RIP analyses, using a sliding-window approach with stringent RIP parameters, implemented simultaneously within the same genetic context, on high quality genome assemblies, yielded superior results in determining the genome-wide RIP among the Ascomycota. Most Ascomycota had RIP and these mutations were particularly widespread among classes of the Pezizomycotina, including the early diverging Orbiliomycetes and the Pezizomycetes. The most extreme cases of RIP were limited to representatives of the Dothideomycetes and Sordariomycetes. By contrast, the genomes of the Taphrinomycotina and Saccharomycotina contained no detectable evidence of RIP. Also, recent losses in RIP combined with controlled TE proliferation in the Pezizomycotina subphyla may promote substantial genome enlargement as well as the formation of sub-genomic compartments. These findings have broadened our understanding of the taxonomic range and extent of RIP in Ascomycota and how this pathway affects the genomes of fungi harboring it.

A chromosome-scale genome assembly of the tomato pathogen Cladosporium fulvum reveals a compartmentalized genome architecture and the presence of a dispensable chromosome

“…S5b and ). As previously reported in other fungi, the Hi-C interaction frequency indicated the approximate location of centromeres [96–99]. In C. fulvum , centromeres are putatively located proximal to chromosome ends (Fig.…”

Tracking of Diversity and Evolution in the Brown Rot Fungi Monilinia fructicola, Monilinia fructigena, and Monilinia laxa

“…The investigation on the genome-wide occurrence of RIP in Monilinia showed that all the three strains showed RIP hallmarks, and that these are likely to be mediated by the RID and DIM-2-mediated DNA methylation pathways ( Gladyshev, 2017 ), as suggested by detection of key genes of these pathways: the two methyltransferases (RID, DIM-2) and the DIM-2-associated cofactors. The only exception was the cofactor DIM-7, which was absent in the Monilinia genomes, in line with what was recently reported for B. cinerea , S. sclerotiorum and several other Ascomycetes ( van Wyk et al, 2021 ). Slight differences among the three genomes were observed in terms of the extent of this phenomenon.…”

Examination of gene loss in the DNA mismatch repair pathway and its mutational consequences in a fungal phylum

“…In addition, there may be other contributing factors to the observed mutational differences between HLT and LLT, such as dysfunction in other DNA repair pathways, loss of methyl transferases, and differences in chromatin structure (Steenwyk, Opulente, et al 2019; Möller et al 2021). For example, previous studies have identified the loss of genes involved in the repeat-induced point (RIP) mutation pathway in powdery mildews (Spanu et al 2010; van Wyk et al 2021). Loss of genes in the RIP pathway in HLT could contribute to the elevated mutation rates we observed relative to LLT.…”