Complete chloroplast genome sequence and characteristics analysis of Qingda no.1 alfalfa (Medicago sativa L. cv. Qingda no.1)

Abstract

<i>Medicago sativa</i> is the most widely cultivated forage legume and one of the most economically valuable crops throughout the world. Qingda no.1 (<i>Medicago sativa </i>L. cv. Qingda no.1) is an excellent alfalfa local variety with strong cold, drought and salt resistance in the three rivers source area of Qinghai. In this study, the whole chloroplast (cp) genome of Qingda no.1 was sequenced, assembled and its structure was analysed by the Illumina high-throughput sequencing technology. The results showed that the chloroplast genome of Qingda no.1 exhibits no obvious typical quadripartite structure; the total length of the chloroplast genome is 125 637 bp; the chloroplast genome contained 111 genes, including 77 protein-coding genes, 30 tRNA genes, and 4 rRNA genes, with an overall GC content of 38.33%. The relative synonymous codon usage showed that 68.67% of the codons RSCU > 1 in Qingda no.1, with the preference ending with A and T. The simple sequence repeat (SSR) analysis identified 62 SSR loci. The phylogenetic analysis of the cp genome, Qingda no.1 clustered closely with <i>Medicago sativa</i> KU321683 (<i>Medicago sativa </i>L. cv. KU321683). These results are helpful for the further study of the Qingda no.1 adaptation mechanism to high altitude stress environments.