van Wyk Stephanie, Wingfield Brenda D, De Vos Lieschen, van der Merwe Nicolaas A, Steenkamp Emma T
Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa.
Front Microbiol. 2021 Feb 1;11:622368. doi: 10.3389/fmicb.2020.622368. eCollection 2020.
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. 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.
重复诱导点（RIP）突变途径是一种真菌特有的基因组防御机制，可减轻重复基因组区域和转座元件（TEs）的有害后果。RIP通过将胞嘧啶转变为胸腺嘧啶来使靶向序列发生突变。我们采用滑动窗口方法研究了RIP在全基因组中的发生情况和程度。利用全基因组RIP数据和两组对照组，对比了有能力和无能力进行RIP的生物体中RIP、TEs和GC含量之间的关联。基于这些数据，我们接着着手确定子囊菌门58个代表物种中RIP的程度和发生情况。通过根据全基因组RIP的程度将每个被研究的真菌归入六个类别之一，总结了研究结果。在高质量基因组组装上，于相同遗传背景下同时采用具有严格RIP参数的滑动窗口方法进行RIP分析，在确定子囊菌门全基因组RIP方面产生了更优结果。大多数子囊菌有RIP，并且这些突变在粪壳菌纲的类别中特别普遍，包括早期分化的圆盘菌纲和盘菌纲。RIP最极端的情况仅限于座囊菌纲和粪壳菌纲的代表物种。相比之下，锤舌菌纲和酵母纲的基因组中没有可检测到的RIP证据。此外，粪壳菌亚门中RIP的近期丧失与TEs增殖受到控制相结合，可能会促进基因组大幅扩大以及亚基因组区室的形成。这些发现拓宽了我们对子囊菌门中RIP的分类范围和程度以及该途径如何影响含有它的真菌基因组的理解。
