Sequence characteristic analyses of the Medicago polymorpha complete chloroplast genome and its codon usage bias

We performed BGISEQ-500 platform sequencing of the chloroplast genome of Medicago polymorpha (JHC, Jiangsu) and assembled its genes using Noveplastys assembly and GeSeq annotation. we then analyzed its sequence characteristics, gene types, codon preferences, and phylogeny using MISA, REPuter, Gview, VISTA tools, IRscope, and DNADnaSP6.0. The JHC chloroplast genome size was 124163 bp. No tetrad structure was observed, and total genomic GC content was 34.09%. A total of 111 genes, including 76 CDS genes, 30 tRNA genes, 4 rRNA genes, and 1 pseudogene, were annotated from the chloroplast genome of JHC. A total of 91 SSR loci and a total of 148 long repeat sequences were also detected. The third position in JHC chloroplast genome codons preferentially used A and U, and UUA, GCU, UAA, ACU, CCU, GAA, GUA, AUU, UGU, GGU, UUU, CUU were the optimal codons of the chloroplast genome of JHC. JHC was closely related to MZ772862 (Yunnan), and was more distantly related to MW971560 (the United States) and NC_ 042848 the United States), indicating that the origins of American and Chinese Medicago polymorpha strains are different.