FIGURE 1 Circular maps for chloroplast genome of six medicinal plants ofPolygonatum . (A) P. zanlanscianense , (B) P. kingianum , (C) P. sibiricum , (D) P. cyrtonema , and (E)P. filipes , (F) P. odoratum . Genes inside and outside the loop are transcribed in a clockwise and anti-clockwise direction. Genes with diverse functions are represented using different colors.

The MISA program was used to identify the SSRs in our study. The total number of SSR sites in the six Polygonatum chloroplast genomes was 64 (P. cyrtonema ) –76 (P. kingianum ), comprising mononucleotide, dinucleotide, trinucleotide, tetranucleotide, and pentanucleotide repeats; only hexanucleotide repeats were found inP. cyrtonema (Figure 2A). Among the SSR sites, the number of mononucleotide repeats was the highest, totaling 242. A/T repeat motifs accounted for the largest proportion, ranging from 97.56% to 100% andP. kingianum , P. filipes and P. odoratum had C/G mononucleotide repeat motifs. A total of 93 dinucleotide repeats were found, with AT/TA accounting for 80%. Trinucleotide repeat sequences were constant in P. odoratum , P. filipes , and P. cyrtonema , whereas ATT and ATA were absent in the other threePolygonatum species. The tetranucleotide and pentanucleotide repeat sequences in the chloroplast genomes of six Polygonatum species were similar. Among them, only P. sibiricum had AAAT tetranucleotide repeat motifs and P. kingianum had one more AATA than the other species (Tables 3 and S2–S7).

A total of 268 repetitive sequences were identified in this study. Palindromic repeats accounted for the largest proportion (51.12 %), followed by forward repeats (36.07 %) and reverse repeats (2.99 %). No complementary repeats were found in the chloroplast genomes of the sixPolygonatum species (Figure 2B). Among these types ofPolygonatum , P. zanlanscianense had significantly longer repetitive sequences than the other species, with 62. P. sibiricum (49), P. cyrtonema (46), P. kingianum (39),P. filipes (36), and P. odoratum (36). Most species were mainly distributed in the IR region. Among them, the number and distribution of all repeat types in P. filipes and P. odoratum were almost the same. The distribution area was mainly in the LSC region and could be distinguished from the others (Tables S8–S13) and the repeat motif size of Polygonatum was mainly concentrated in the range of 30–39 bp (Figure S2).

TABLE 2 List of genes found in the chloroplast genomes of six medicinal plants of Polygonatum .