International Year of Plant Health: FABI embraces the 4IR with technology that unravels the genetics behind fungal genome evolution

16 July 2020

In the age of genomics and bioinformatics scientists can produce massive amounts of data on deadly fungi threatening biodiversity and agriculture.

According topostdoctoral fellow at the University of Pretoria’s (UP) Forestry and Agricultural Biotechnology Institute (FABI), Dr Stephanie van Wyk, “Over the last 30 years great strides have been made in fungal genomic research, from identifying and unravelling a gene at a time, to being able to read the entire genomic sequence of particular organisms. This has resulted in lots of genetic data which, until recently, was all manually processed and analysed.”

FABI researchers in the field

The greatest challenge lies in processing these vast quantities of data to allow us to develop sustainable strategies to eradicate harmful fungi which threaten our food security and plant health. With the fourth industrial revolution (4IR) upon us, a team of researchers at FABI set out to bridge this gap.

“We wanted to look at genomic research from a big picture and be able to build a puzzle from what we already knew. Much like looking at the puzzle box and figuring out which parts go where, we had to build a framework for scientists to use as a resource. UP is one of the top research universities in the world for mycology and fungal genomics so we were in a very strong position to develop this software,” said Dr Van Wyk.

FABI researchers in the field

One of their major research outputs included developing a set of software tools that automate labour-intensive techniques to study a gene mutation processes unique to fungi. It’s called repeat-induced point mutation (RIP) analyses. RIP analyses have proven insightful in exploring the evolutionary history of genomic regions underlying important biological traits such as host range, lifestyle and pathogenicity.

Enter the RIPper, a bioinformatic software tool that’s developed by researchers at FABI, which applies these techniques to fungal genome sequences, allowing scientist to unravel important evolutionary implications for fungi. 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. “At UP, we believe in doing research that benefits society as a whole and we believe in making our research as accessible as possible. The RIPper is free to use and since it’s web-based, it’s circumvented the need for every scientist to have access to vast amounts of computational power, servers and licence agreements,” said Dr Van Wyk.

The RIPper’s ability to visualise RIP and retrieve the data produced in different formats, puts this software at the forefront of bioinformatic applications. 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.

“With our software, we realised that a fungi which was plaguing SA’s pine forests was evolving at a much faster rate than we’d originally anticipated. Our pine forests carry considerable commercial implications in SA and a pathogenic fungi destroying them has major economic consequences for us,” said Dr Van Wyk.

“We currently have 322 RIPper users from 22 countries including South Africa, USA, Germany, Australia, Canada, Switzerland, France, United Kingdom, Taiwan, Brazil, Ireland, Italy, Japan, South Korea, Netherlands, China and India. The RIPper has facilitated discussions with top universities focusing on genome evolution which lays the groundwork for further international research collaborations. These universities include the Christian-Albrechts University of Kiel and Max Planck Institute of Evolutionary Biology, Kiel and Ploen, Germany and University of Neuchâtel.

Watch this video to understand exactly how the RIPper works.

Different types of pathogenic fungi