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New Analysis Sheds Light on Specific Genes Found in All Grasses
Research identifies over 13,000 groups of genes highly conserved in all grasses of which 4,609 were identified as lineage specific
22 April, 2025
A new computational biology pipeline has mapped out over 13,000 groups of protein-coding genes conserved across grasses, offering a powerful tool for researchers investigating gene function in these economically and ecologically vital species.
Drawing on genomic data from 16 fully sequenced grass species within Ensembl Plants, the study identified 13,312 highly conserved "universal" groups of grass genes. These gene groups are present across all studied grasses and the genes within groups are highly similar suggesting they are responsible for vital functions in all grasses.
Crucially, the pipeline’s findings held up under scrutiny: 98.8% of these groups were also detected in newly sequenced genomes from two major grass groups (clades) not included in the original analysis, underscoring the robustness of the approach.
I hope the research community will find it useful to accelerate progress in grass genetics, including efforts to improve yield, stress resistance, and nutrient use in cereals like rice, wheat, and maize.
The study also identified 4,609 gene groups likely involved in functions specific to monocots, commelinids, or grasses — a significant step toward untangling the evolution of traits that led to the evolutionary success of the grasses.
What sets this study apart is its use of a statistical technique known as the Hidden Markov Model (HMM), which emphasises the conserved parts of genes which are important for function rather than the whole sequence. This technique outperformed a simpler approach based on percentage identity of sequence in distinguishing between known lineage-specific and non-specific genes.
Researchers working on gene discovery such as QTL analysis in grasses can now consult the newly released universal_grass_peps database to determine whether their genes of interest are conserved across the grass family and whether they are potentially linked to lineage-specific adaptations.
“The database offers a new source of information for grass genes of unknown function, conveniently identifying those that are common to all grasses and how grass-specific their function is likely to be.” said the study’s author, Rothamsted’s Dr Rowan Mitchell. “I hope the research community will find it useful to accelerate progress in grass genetics, including efforts to improve yield, stress resistance, and nutrient use in cereals like rice, wheat, and maize.”
(AI generated image: Canva)
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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,
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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).
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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
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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.
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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.