RIFinder reveals widespread adaptive remote introgression in grass genomes

作者：Yujie Huang, Shiyu Zhang, Hanyang Lin, Chenxu Liu, Z. K. Li, Kun Yang, Yutong Liu, Linfeng Jin, Chuanlong Lu, Yuan Cheng, Chaoyi Hu, Huifang Zhao, Guoping Zhang, Qian Qian, Longjiang Fan, Dongya Wu · 发表于：Plant Communications · 年份：2025 · DOI：10.1016/j.xplc.2025.101658 · 被引用次数：1 · 研究领域：Chromosomal and Genetic Variations、Genetic diversity and population structure、Genomics and Phylogenetic Studies

Genetic transfers are pervasive across both prokaryotes and eukaryotes, primarily involving canonical genomic introgression between species or genera and horizontal gene transfer (HGT) across kingdoms. However, DNA transfer between phylogenetically distant species, which differs from canonical introgression and HGT in certain aspects of its temporal scale and mechanistic features, here defined as remote introgression (RI), has received less attention in evolutionary genomics. In this study, we present RIFinder, a novel phylogeny-based method for the detection of RI events, and apply it to a comprehensive dataset of 122 grass genomes. Our analysis identifies 622 RI events originating from 543 distinct homologous genes, revealing distinct characteristics among grass subfamilies. Specifically, the subfamily Pooideae contains the largest number of introgressed genes, whereas Bambusoideae contains the fewest. Comparisons among the accepted genes, their donor copies, and native homologs demonstrate that introgressed genes undergo post-transfer localized adaptation and show significant functional enrichment in stress-response pathways. Notably, we identify a large Triticeae-derived segment in the Chloridoideae species Cleistogenes songorica, which is potentially associated with its exceptional drought tolerance. Furthermore, we provide compelling evidence that RI has contributed to the origin and diversification of biosynthetic gene clusters for gramine, a defensive alkaloid chemica...