Complete Chloroplast Genome Sequence of <em>Medicago falcata</em>: Comparative Analyses with Other Species of <em>Medicago</em>

Medicago falcata is one of the most important perennial forage legumes in the Medicago genus. In this study, we reported the complete chloroplast genome of two M. falcata ecotypes grown in different regions, and compared them with those of Medicago truncatula and Medicago sativa. We found that M. falcata genome contains 78 protein-coding genes, 30 tRNA genes, and 4 ribosomal RNA genes, with only one copy of the inverted repeat. They shared high conservation in size, genome structure, gene order, gene number and GC content with those of M. truncatula and M. sativa. High nucleotide diversity occurred in the coding gene regions of rps16, rps3 and ycf4 genes. Meanwhile, mononucleotide repeats are the most abundant repeat type, followed by the di-, tri-, tetra-, and pentanucleotides, and forward repeats were more abundant than reverse and palindrome repeats for all these three Medicago species. Phylogenetic analysis based on both coding sequences and complete chloroplast genome sequences demonstrated that M. falcata had the closest relationship with M. hybrid and M. sativa. This study provided valuable information for further studies on the genetic relationship of the Medicago genus.