Abstract:In order to explore the chloroplast genome characteristics and codon bias of Polygonatum kingianum, the next generation sequencing technology was utilized to sequence the young leaves, and the complete chloroplast genome sequence was obtained after assembly and annotation. SSR loci, phylogeny and codon preference of the chloroplast genome were analyzed by MISA, Emboss and Codonw software. The results showed that the length of complete chloroplast genome sequence of P. kingianum was 155 852 bp, including a pair of inverted repeats of 26 347 bp that were separated by large and small single copy regions (LSC, 84 633 bp and SSC, 18 525 bp). A total of 132 genes were annotated in the chloroplast genome, including 86 protein-coding genes, 8 rRNA genes and 38 tRNA genes. The average GC content of chloroplast genomes was 37.7%. A total of 69 SSR loci were detected, most of which belonged to single-base repeat A/T type. Phylogenetic analysis showed that P. kingianum was closer to P. tessellatum than other species, which may be related to their geographical distribution. The chloroplast genome codon usage pattern was more influenced by natural selection than mutation, and 9 codons were identified as the optimal codon. Therefore, these would provide important reference information for exploring the genetic relationship and the improvement of exogenous genes in P. kingianum.