Chloroplast Genome Sequencing and Comparative Analysis of Six Medicinal Plants of <i>Polygonatum</i>

The genus <i>Polygonatum</i> boasts abundant germplasm resources and comprises numerous species. Among these, medicinal plants of this genus, which have a long history, have garnered attention of scholars. This study sequenced and analyzed the chloroplast genomes of six species of <i>Polygonatum</i> medicinal plants (<i>P. zanlanscianense</i>, <i>P. kingianum</i>, <i>P. sibiricum</i>, <i>P. cyrtonema</i>, <i>P. filipes</i>, and <i>P. odoratum</i>, respectively) to explore their interspecific relationships. The sequence length (154, 578-155, 807 bp) and genome structure were conserved among the six <i>Polygonatum</i> species, with a typical tetrad structure. Among the 127-131 genes contained in the genomes, 84-85 are protein-coding genes, 37-38 are transfer RNA genes, and 6-8 are ribosomal RNA genes. The genomes contained 64-76 simple sequence repeats (SSRs) and 36-62 long repetitive sequences. Codon bias patterns tended to use codons ending in A/T. In 30 types of codons with RSCU > 1, 93.3% ended in A/T of the six species. Twenty-one highly variable plastid regions were identified in the chloroplast genomes of the six medicinal plants. Furthermore, a phylogenetic analysis encompassing these and 53 other chloroplast genomes of <i>Polygonatum</i> species revealed that <i>P. cyrtonema</i>, <i>P. odoratum</i>, and <i>P. filipes</i> clustered together on one clade, whereas <i>P. kingianum</i> and <i>P. zanlanscianense</i> formed separate clades. Notably, <i>P. sibiricum</i> emerged as a standalone clade, and our phylogenetic tree reinforces the classification of <i>P. sibiricum</i> as forming a monophyly. This study provides a novel basis for intragenus taxonomy and DNA barcoding molecular identification within the genus <i>Polygonatum</i> medicinal plants.