Genomic resources for Medicago archiducis-nicolai and Medicago ruthenica

Wild perennial sister species Medicago archiducis-nicolai (rhizomatous/alpine) and M. ruthenica2(non-rhizomatous/xeric) constitute vital genetic resources for forage improvement. To decode the3genomic basis of their contrasting trait and habitat adaptation, we generated chromosome-scale4genome assemblies, resequenced 128 individuals, profiled transcriptomes under cold/heat stress,5and functionally validated causal alleles. We demonstrate that structural variations (SVs)—6particularly gene duplications—are primary drivers of rhizome development and alpine/xeric7adaptation. Further, pervasive presence-absence SVs (PAVs) in noncoding regulatory regions8underpin divergent allele-specific expression governing rhizome formation and stress responses.9Crucially, these regulatory PAVs induce contrasting expression patterns during trait development10and stress adaptation. Our findings reveal a dual mechanism whereby coding and regulatory SVs11convergently orchestrate phenotypic innovation and ecological specialization in sister species,12offering valuable genomic resources for legume evolution studies and alfalfa breeding.