High-quality genome assemblies of wheat wild relatives Thinopyrum intermedium and Roegneria kamoji revealed different polyploid genome evolution paths

Intermediate wheatgrass (Thinopyrum intermedium (Host) Barkworth & D.R. Dewey, syn. Trichopyrum intermedium (Host) Á.Löve; 2n = 6x = 42) and Roegneria kamoji (Ohwi) Keng & S.L.Chen (syn. Campeiostachys kamoji (Ohwi) B.R.Baum, J.L.Yang & C.Yen; Elymus kamoji (Ohwi) S.L.Chen; 2n = 6x = 42) are allohexaploid perennial species within the Triticeae family and are recognized as critical genetic resources for wheat improvement and forage breeding. We performed whole genome sequencing and assembly by combining PacBio HiFi and high-throughput chromosome conformation capture sequencing (Hi-C) sequencing technologies to elucidate the evolutionary paths of these species and enhance wheat breeding efforts. By integrating phylogenetic inferences and functional analyses, we aimed to address longstanding taxonomic uncertainties and assess the role of wild Triticeae species as genetic reservoirs of disease-resistance traits.