The RIPper, a web-based tool for genome-wide quantification of Repeat-Induced Point (RIP) mutations

Stephanie van Wyk; Christopher H Harrison; Brenda D Wingfield; Lieschen De Vos; Nicolaas A van der Merwe; Emma T Steenkamp

doi:10.7717/peerj.7447

The RIPper, a web-based tool for genome-wide quantification of Repeat-Induced Point (RIP) mutations

PeerJ. 2019 Aug 26:7:e7447. doi: 10.7717/peerj.7447. eCollection 2019.

Authors

Stephanie van Wyk¹, Christopher H Harrison², Brenda D Wingfield¹, Lieschen De Vos¹, Nicolaas A van der Merwe¹, Emma T Steenkamp¹

Affiliations

¹ Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, Gauteng, South Africa.
² Department of product and software development, Amplo PTY, Pretoria, Gauteng, South Africa.

Abstract

Background: The 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.

Results: We 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.

Conclusion: This 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.

Keywords: Fine-scale RIP analyses; Genome-wide quantification; Large RIP affected regions; RIP; RIP profile; Repeat-Induced Point mutations; The RIPper; Web-based tool.

Grants and funding

This work is based on research funded and supported in part by the South African National Department of Science and Technology (DST), National Research Foundation (South Africa) as well as the University of Pretoria and the Tree Protection Cooperative Programme (TPCP) with regards to student funding. There was no additional external funding received for this study. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.