Evolution of paleo‐duplicated chromosome pairs with enrichment of NBS ‐LRR genes generated through ρ‐ WGD in Poaceae

In Poaceae, the rho whole-genome duplication (ρ-WGD) event gave rise to three Paleo-duplicated chromosome pairs (PdCPs) that are enriched in resistance genes (nucleotide-binding site-leucine-rich repeat (NBS-LRR) genes) but show low transcriptional levels. Despite their evolutionary importance, systematic family-wide studies of PdCPs have been lacking. We analyzed 37 Poaceae genomes using karyotyping and evolutionary analyses, mapped NBS-LRR genes distributions, and examined transcriptomic and epigenomic patterns across representative species to characterize the evolution and regulation of PdCPs. Our findings show that PdCPs have persisted throughout the evolutionary history of Poaceae, exhibiting distinct patterns of rearrangements among different subfamilies. Notably, one PdCPs is consistently enriched in disease resistance genes across multiple subfamilies and displays conserved low transcriptional activity. This PdCPs also exhibits conserved CHH hypomethylation around transcription start site regions. Further analyses suggest that this PdCPs maintains a more closed chromatin state, associated with repressive histone modifications that suppress gene expression. These results imply that the low transcriptional levels of genes on this PdCPs may be regulated by multiple epigenetic mechanisms. This study advances our understanding of the formation, diversification, and epigenetic regulation of PdCPs following the ρ-WGD in Poaceae.