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Fungal genome secrets unlocked in breakthrough for crop disease research
Advanced genome mapping of septoria leaf blotch fungus could lead to improved control strategies
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.”
Publication
Contacts
Dr Jason Rudd
Molecular Plant Pathologist
ABOUT ROTHAMSTED RESEARCH
Rothamsted Research is the longest-running agricultural research institute in the world. We work from gene to field with a proud history of ground-breaking
discoveries in areas as diverse as crop management, statistical interpretation and soil health. Our founders, in 1843, were the pioneers of modern
agriculture, and we are known for our imaginative science and our collaborative approach to developing innovative farm practice.
Through independent research, we make significant contributions to improving agri-food systems in the UK and internationally, with
economic impact estimated to exceed £3 bn in annual contribution to the UK economy. Our strength lies in our systems approach, which combines strategic research,
interdisciplinary teams and multiple partnerships.
Rothamsted is home to three unique National Bioscience Research Infrastructures which are open to researchers from all over the world:
The Long-Term Experiments,
Rothamsted Insect Survey and the
North Wyke Farm Platform.
We are strategically funded by the Biotechnology and Biological Sciences Research Council (BBSRC), with additional support from other national and
international funding streams, and from industry. We are also supported by the Lawes Agricultural Trust (LAT).
ABOUT BBSRC
The Biotechnology and Biological Sciences Research Council is part of UK Research and Innovation, a non-departmental public body funded by a grant-in-aid
from the UK government.
BBSRC invests to push back the frontiers of biology and deliver a healthy, prosperous and sustainable future. Through our investments, we build and support a vibrant,
dynamic and inclusive community which delivers ground-breaking discoveries and develops bio-based solutions that contribute to tackling global challenges,
such as sustainable food production, climate change, and healthy ageing.
As part of UK Research and Innovation (UKRI), we not only play a pivotal role in fostering connections that enable the UK’s world-class research and innovation system
to flourish – we also have a responsibility to enable the creation of a research culture that is diverse, resilient, and engaged.
BBSRC proudly forges interdisciplinary collaborations where excellent bioscience has a fundamental role. We pioneer approaches that enhance the equality, diversity,
and inclusion of talent by investing in people, infrastructure, technologies, and partnerships on a global scale.
ABOUT LAT
The Lawes Agricultural Trust, established in 1889 by Sir John Bennet Lawes, supports Rothamsted Research’s national and international agricultural science through the provision of land, facilities and funding. LAT, a charitable trust, owns the estates at Harpenden and Broom's Barn, including many of the buildings used by Rothamsted Research. LAT provides an annual research grant to the Director, accommodation for nearly 200 people, and support for fellowships for young scientists from developing countries. LAT also makes capital grants to help modernise facilities at Rothamsted, or invests in new buildings.