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.
Highlights
The Ascomycota represents the largest taxonomic division of the fungal kingdom and includes a vast collection of diverse species (Schoch et al, 2009)
To evaluate the influence of assembly quality and genome completeness on the genome-wide Repeat-Induced Point (RIP) statistics obtained for a particular organism, three versions (2012, 2018, and 2020) of the genome assembly for F. circinatum isolate FSP34 were used (Table 1)
These data show that the effects of RIP in a particular fungal genome would be underestimated if low-quality genome sequences are used in the analysis
Summary
The Ascomycota represents the largest taxonomic division of the fungal kingdom and includes a vast collection of diverse species (Schoch et al, 2009). These fungi are ubiquitous and can be found in all environmental settings where they are key players in the recycling of organic matter in aquatic and terrestrial systems (Mueller and Schmit, 2007). RIP in the Ascomycota medical and economic importance, certain Ascomycota are exploited for their industrial and commercial properties (de Oliveira and de Graaff, 2011; Grigoriev et al, 2011) Their products are essential in fermentation processes and the production of sought after foods and products, such as meat alternatives (Kumar et al, 2017), biofuels (Grigoriev et al, 2011), organic chemicals (Payne et al, 2015), enzymes, and antibiotics (Martens and Demain, 2017)
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