Abstract
BackgroundThe RIPper (http://theripper.hawk.rocks) is a set of web-based tools designed for analyses of Repeat-Induced Point (RIP) mutations in the genome sequences of Ascomycota. The RIP pathway is a fungal genome defense mechanism that is aimed at identifying repeated and duplicated motifs, into which it then introduces cytosine to thymine transition mutations. RIP thus serves to deactivate and counteract the deleterious consequences of selfish or mobile DNA elements in fungal genomes. The occurrence, genetic context and frequency of RIP mutations are widely used to assess the activity of this pathway in genomic regions of interest. Here, we present a bioinformatics tool that is specifically fashioned to automate the investigation of changes in RIP product and substrate nucleotide frequencies in fungal genomes.ResultsWe demonstrated the ability of The RIPper to detect the occurrence and extent of RIP mutations in known RIP affected sequences. Specifically, a sliding window approach was used to perform genome-wide RIP analysis on the genome assembly of Neurospora crassa. Additionally, fine-scale analysis with The RIPper showed that gene regions and transposable element sequences, previously determined to be affected by RIP, were indeed characterized by high frequencies of RIP mutations. Data generated using this software further showed that large proportions of the N. crassa genome constitutes RIP mutations with extensively affected regions displaying reduced GC content. The RIPper was further useful for investigating and visualizing changes in RIP mutations across the length of sequences of interest, allowing for fine-scale analyses.ConclusionThis software identified RIP targeted genomic regions and provided RIP statistics for an entire genome assembly, including the genomic proportion affected by RIP. Here, we present The RIPper as an efficient tool for genome-wide RIP analyses.
Highlights
The Repeat-Induced Point (RIP) mutation pathway is a genome defense mechanism that has evolved exclusively in fungi (Gladyshev, 2017)
We demonstrate The RIPper’s ability to detect RIP in fungal sequences by performing RIP analyses on the genome assembly of Neurospora crassa, as well as on gene regions, transposable elements (TEs), and large genomic regions previously shown to be affected by RIP
To investigate the influence of GC content composition on RIP statistics, simulated sequences consisting of different GC content ranges were subjected to RIP analysis using varying degrees of stringency of the RIP parameters
Summary
The Repeat-Induced Point (RIP) mutation pathway is a genome defense mechanism that has evolved exclusively in fungi (Gladyshev, 2017). RIP distinguishes genetic targets based on shared homology between the repeats and permanently mutates them by inducing cytosine to thymine transition mutations (Selker et al, 1987) This mutational process is coupled with epigenetic silencing of the RIP affected regions (via methylation of the remaining cytosine residues) to further attenuate the deleterious effects of TEs (Selker et al, 2003). Fine-scale analysis with The RIPper showed that gene regions and transposable element sequences, previously determined to be affected by RIP, were characterized by high frequencies of RIP mutations. Data generated using this software further showed that large proportions of the N. crassa genome constitutes RIP mutations with extensively affected regions displaying reduced GC content. We present The RIPper as an efficient tool for genome-wide RIP analyses
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