Genomic analysis of Medicago ruthenica provides insights into its tolerance to abiotic stress and demographic history

Medicago ruthenica has been recently cultivated as a new forage crop and has been recognized as a source of genes to improve abiotic stress tolerance in cultivated alfalfa because of its remarkable tolerance to drought, salinity-alkalinity, and cold and snowy winters. Here, we reveal a chromosome-scale genome sequence of M. ruthenica based on Illumina, PacBio, and Hi-C data. The assembled genome consists of 903.56 Mb with 50,268 annotated protein-coding genes, which is larger and contains relatively more genes than Medicago truncatula (420 Mb and 44,623 genes) and Medicago sativa spp. caerulea (793 Mb and 47,202 genes). All three species shared the ancestral Papilionoideae whole-genome duplication event before their divergence. The more recent expansion of repetitive elements compared to that in the other two species was determined to have contributed greatly to the larger genome size of M. ruthenica. We further found that multiple gene and transcription factor families (e.g., SOS homologous genes, NAC, C2H2, and CAMTA) have expanded in M. ruthenica, which might have led to its enhanced tolerance to abiotic stress. In addition, M. ruthenica harbors more genes involved in the lignin and cellulose biosynthesis pathways than the other two species. Finally, population genomic analyses revealed two genetic lineages, reflecting the west and east of its geographical distribution, respectively. The two lineages probably diverged during the last glaciation and survived in multiple refugia at the last glacial maximum, followed by recent expansion. Our genomic data provide a genetic basis for further molecular breeding research on M. ruthenica and alfalfa.