Widespread remote introgression in the grass genomes

Abstract

Genetic transfers are pervasive across both prokaryotes and eukaryotes, encompassing canonical genomic introgression between species or genera and horizontal gene transfer (HGT) across kingdoms. However, DNA transfer between phylogenetically distant species, here defined as remote introgression (RI), has remained poorly explored in evolutionary genomics. In this study, we present RIFinder, a novel phylogeny-based method for RI event detection, 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 exhibits the highest number of introgressed genes while Bambusoideae contains the lowest. Comparisons among accepted genes, their donor copies and native homologs demonstrate that introgressed genes undergo post-transfer localized adaptation, with significant functional enrichment in stress-response pathways. Notably, we identify a large Triticeae-derived segment in a 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 of gramine, a defensive alkaloid chemical, across grass species. Collectively, our study establishes a robust method for RI detection and highlights its critical role in adaptive evolution.