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Background   Medicago ruthenica , a wild and perennial legume forage widely distributed in semi-arid grasslands, is distinguished by its outstanding tolerance to environmental stress. It is a close relative of commonly cultivated forage of alfalfa ( Medicago sativa ). The high tolerance of  M. ruthenica  to environmental stress makes this species a valuable genetic resource for understanding and improving traits associated with tolerance to harsh environments.    Results  We sequenced and assembled genome of  M. ruthenica  using an integrated approach, including PacBio, Illumina, 10×Genomics, and Hi-C. The assembled genome was 904.13 Mb with scaffold N50 of 99.39 Mb, and 50,162 protein-coding genes were annotated. Comparative genomics and transcriptomic analyses were used to elucidate mechanisms underlying its tolerance to environmental stress. The expanded  FHY3/FAR1  family was identified to be involved in tolerance of  M. ruthenica  to drought stress. Many genes involved in tolerance to abiotic stress were retained in  M. ruthenica  compared to other cultivated  Medicago  species. Hundreds of candidate genes associated with drought tolerance were identified by analyzing variations in single nucleotide polymorphism using accessions of  M. ruthenica  with varying tolerance to drought. Transcriptomic data demonstrated the involvements of genes related to transcriptional regulation, stress response, and metabolic regulation in tolerance of  M. ruthenica.Conclusions  We present a high-quality genome assembly and identification of drought-related genes in the wild species of  M. ruthenica , providing a valuable resource for genomic studies on perennial legume forages.    Supplementary Information  The online version contains supplementary material available at 10.1186/s12915-021-01033-0.

The genome of a wild Medicago species provides insights into the tolerant mechanisms of legume forage to environmental stress