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.
3.2 | Simple sequence
repeats and interspersed repeats sequences
analysis
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 .