Natural Science Foundation of Shanghai (18ZR1425400)
Medicago L. is a genus comprising approximately 87 species in the world, and 15 species in China. Most of them are widely distributed and can live in different habitats. Due to complex morphological variation such as pods, and diverse breeding systems, the evolutionary history of this genus has always been one of the hotspot. With the development of molecular ecology, the use of genomics to solve ecological problems has been continuously reported. However, the current chloroplast genome data of the genus of Medicago in China is still lacking, and the analysis of its evolution path has seldom carried out. In this study, ten Medicago species and one Trigonella species in China were selected to sequence and compare the structural characteristics of the chloroplast genomes. The phylogenetic relationship based on the chlroplast genome and nuclear ITS sequence were analyzed, and the evolution path were explored based on their geographical distribution and habitat characteristics. The results showed that the chloroplast genomes of the above species were 121-127 kb in size, all of which displayed atypical quadripartite structure missing one copy of the inverted repeat region (IR). Totally, 1,273 variable SSR loci were found in these Medcago species, which could be used as potential molecular markers to identify Medicago germplasms. There were 6 inversions happened in the chloroplast genome of the tested Medicago species. Two unique inversions were identified between genes atpB to ycf3, ndhC to trnLUAA in M. lupulina. And four inversions were shared by M. archiducis-nicolai and M. ruthenica between genes psbM to psaA, ndhB to trnNGUU, ndhB to rpoA, clpP to rpl20. Intron losses were also observed in clpP, rpoC1 and atpF genes in M. lupulina chlroplast plastome. The phylogenetic relationship based on chloroplast genome and ITS sequences supported the traditional classification to subdivide Chinese Medicago into section Medicago, Spirocarpos, Platycarpae and Lupularia. The basal position of the clade consisting of M. edgeworthii, M. orthoceras and M. monantha like the Trigonella supported the existence of ″Trigonelloid″ Medicago. The differentiation may be related to the habitats of these species, especially the annual average temperature may be the decisive factor leading to the differentiation of Medicago in China.