Fungal genome secrets unlocked in breakthrough for crop disease research

An international team of scientists, including from Rothamsted Research, have developed a new method to improve the accuracy of gene mapping in complex organisms—a breakthrough that could enhance research into fungal diseases affecting crops like wheat.

Using an advanced bioinformatics tool, researchers have re-annotated the genome of Zymoseptoria tritici, a major fungal pathogen responsible for septoria leaf blotch—a disease that causes significant wheat yield losses across Europe. Their findings highlight major flaws in previous genetic analyses and offer a more precise picture of the fungus’s genetic structure.

Until now, predicting genes in complex organisms has been a challenge, even with vast amounts of genetic data available. Past efforts to map the genes of Z. tritici produced inconsistent results, with different studies identifying between 10,900 and 13,200 genes, yet only a third of these findings matched across datasets.

To address this, the research team developed InGenAnnot, a tool that combines multiple gene prediction methods with real biological evidence from fungal RNA sequences. The updated analysis identified 13,414 high-confidence genes, improving the accuracy of previous research and shedding new light on how the fungus regulates its genes.

The team, led by French scientists from INRAE, compared four different gene prediction datasets for the same Septoria strain, each generated independently by researchers in the Netherlands, Germany, USA, Australia and the UK (Rothamsted Research).

Dr Jason Rudd who led Rothamsted’s contribution to the study, said “Whilst many differences were observed, when each gene was analysed in detail, we were able to form a consensus on the most accurate structure of each and every one of them, as well as identify previously hidden genes, and structural gene variants”.

This has given rise to the release of a “gold standard” open community reference resource for this important fungus which will accelerate research efforts to identify exploitable weaknesses in the pathogen.

The study also revealed new insights into how the pathogen’s genes are structured and expressed, particularly in regions that influence when and how genes are activated. This could help scientists better understand how the fungus adapts in wheat to different environments potentially paving the way for more effective disease control strategies.

“Accurate genome mapping is a crucial step in tackling fungal diseases, which are becoming an increasing threat to global food security,” said Dr Rudd. “By refining gene prediction techniques, we hope we can improve our ability to monitor and combat these pathogens before they cause further damage to crops.”