FABI technology unravels the genetics behind fungal genome evolution
A team of FABI researchers (Ms. Stephanie van Wyk, Prof Emma Steenkamp, Prof Brenda Wingfield, Dr Able van der Merwe and Dr Lieschen De Vos) set out to investigate a mutational process that has important evolutionary implications for fungi. But they were soon faced with a problem: Even though the bioinformatic data was readily available, there were no appropriate software tools to apply to their investigation. To overcome this challenge, they developed a bioinformatics tool called The RIPper.
The strength of this software lies in the automation of laborious techniques to study the mutation process called Repeat-Induced Point mutations (RIP). The RIPper applies these techniques to fungal genome sequences, allowing conclusive results within minutes. Fine-scale RIP analyses have proven insightful in exploring the evolutionary history of genomic regions underlying important biological traits such as host range, lifestyle and pathogenicity. The greatest advantage of this program is the ability to easily produce a RIP profile for each genome. In essence, a RIP profile describes the extent of RIP and provides genomic context of this mutational process for each fungus investigated. This software was specifically designed to be user-friendly and was fashioned as a web-based tool to ensure accessibility to the broader scientific community (https://theripper.hawk.rocks). The RIPper’s ability to visualise RIP and retrieve the data produced in different formats, puts this software at the forefront of bioinformatic applications (video).
This innovative pipeline now allows for an exciting era to investigate RIP on a genome-wide scale to answer pressing questions relating to pathogen development and genome evolution.