Characterization of the complete chloroplast genome of alfalfa (Medicago sativa) (Leguminosae)

Alfalfa is the most widely cultivated forage legume and one of the most economically valuable crops throughout the world. We sequenced the complete chloroplast genome of alfalfa, which is 128,574 bp in size and contains only one copy of the inverted repeat (IR) in the results from the second generation of high-throughput sequencing platform, Illumina HiSeq 2000. The genome encodes 109 genes, including 4 ribosomal RNA genes, 30 tRNAs, and 75 protein-coding genes. The genes rps16, ycf4, and infA are absent in the alfalfa chloroplast genome, and ndhB has an internal stop codon in the 5′ exon, which is similar to what is observed in other legumes. The rps12 gene, minus its intron, is a trans-spliced gene with the 5′ end located in the LSC region, and the duplicated 3′ end is located in the IR regions. Relative to other legume chloroplast genomes, the alfalfa genome differs in total length, IR length, GC content, the number of total genes and the number of functional genes (including protein genes, pseudogenes, rRNA genes, and tRNA genes). Phylogenetic analysis based on 5 chloroplast genes demonstrates a close relationship between alfalfa and Medicago hybrida and provides strong support for the IRLC group. These results provide a solid foundation for chloroplast molecular biology and genetic breeding and molecular evolution of alfalfa.