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RIFinder reveals widespread adaptive remote introgression in grass genomes
Yujie Huang1, Shiyu Zhang1, Hanyang Lin2
1Institute of Crop Science, Zhejiang University, Hangzhou, China.
Plant Communications
|December 7, 2025
Summary
Remote introgression (RI) is a key evolutionary process in grasses, involving DNA transfer between distant species. This study introduces RIFinder, a new tool to detect RI events, revealing their role in adaptation and gene evolution.
Area of Science:
- Evolutionary genomics
- Molecular evolution
- Bioinformatics
Background:
- Genetic transfers, including horizontal gene transfer (HGT), are common but remote introgression (RI) between distant species is less understood.
- RI differs from canonical introgression and HGT in temporal scale and mechanisms.
- Understanding RI is crucial for evolutionary genomics.
Purpose of the Study:
- To develop and apply a novel phylogeny-based method, RIFinder, for detecting remote introgression (RI) events.
- To investigate the prevalence and characteristics of RI in grass genomes.
- To explore the functional and evolutionary implications of RI in grasses.
Main Methods:
- Development of RIFinder, a phylogeny-based computational method for RI detection.
- Application of RIFinder to a dataset of 122 grass genomes.
- Comparative analysis of introgressed genes, donor copies, and native homologs.
Main Results:
- Identified 622 RI events from 543 homologous genes across 122 grass genomes.
- Pooideae showed the highest number of introgressed genes, while Bambusoideae had the fewest.
- Introgressed genes are enriched in stress-response pathways and contribute to gramine biosynthesis.
- Discovered a Triticeae-derived segment in Cleistogenes songorica potentially linked to drought tolerance.
Conclusions:
- RI is a significant factor in grass adaptive evolution and genome diversification.
- RI contributes to the evolution of stress tolerance and secondary metabolite production.
- RIFinder provides a robust method for detecting RI events, advancing evolutionary genomics research.
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