Complete Chloroplast Genome Sequence of Medicago falcata: Comparative Analyses with Other Species of Medicago

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 the M. falcata chloroplast genome lacks a typical quadripartite structure, containing 78 protein-coding genes, 30 tRNA genes, and four ribosomal RNA genes. 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 analyses using both coding sequences and complete chloroplast genomes revealed that M. falcata shares the closest phylogenetic relationship with M. hybrida and M. sativa. This study provided valuable information for further studies on the genetic relationship of the Medicago genus.