Comparative And Population Genomics Of Medicago Ruthenica

Medicago ruthenica Trautv.(2n = 2x =16)belonging to the genus Medicago L.of Papilionoideae,Leguminosae,is widely distributed in northern China,Mongolia,and eastern Siberia.M.ruthenica has been recently cultivated as a new forage crop because of its rich protein and mineral content,excellent palatability as well as easy digestion,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.However,to date,only three reference genomes(Medicago truncatula,Medicago polymorpha and Medicago sativa)of this genus are reported,which severely hinders the evolutionary genomic study of Medicago and the molecular breeding research on M.ruthenica and alfalfa.In this study,we de novo assembled a high-quality chromosome-level reference genome of M.ruthenica,and performed genome annotation,comparative genomics analysis and population genomics analysis based on whole genome sequencing data.The main results are summarized as follows:(1)We reveal a chromosome-scale genome sequence of M.ruthenica based on Illumina,Pac Bio,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 M.truncatula(420 Mb and 44,623 genes),M.sativa spp.caerulea(793Mb and 47,202 genes)and M.polymorpha(457Mb and 36,087 genes).(2)Comparative genomics analyses revealed that all the Medicago species shared the ancestral Papilionoideae whole-genome duplication event before their divergence.The more recent expansion of repetitive elements compared to that in M.truncatula and M.sativa 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 M.truncatula and M.sativa.(3)Population genomic analyses based on whole-genome resequencing data revealed two genetic lineages,reflecting the west and east of its geographical distribution,respectively.Population history reconstruction and species distribution models indicated that the two lineages likely diverged during the last glaciation and survived in multiple refugia at the last glacial maximum,followed by recent effective population expansion.Our genomic data provide a valuable resource for investigating the genome evolution of Medicago and a genetic basis for further molecular breeding research on M.ruthenica and alfalfa.