Molecular identification and phylogenetic analysis of Polygonatum Kingianum with different floral colors on the basis of chloroplast genomes.

Polygonatum kingianum, a plant with both medicinal and edible properties, demonstrates considerable variation in perianth coloration, making its differentiation from related species through morphological characteristics particularly challenging. This variation has led to frequent substitution of P. kingianum with other Polygonatum species in commercial markets, thereby compromising product quality and posing risks to the safety and efficacy of clinical applications. This research reports the sequencing and assembly of chloroplast genomes from three P. kingianum phenotypes with distinct floral colors. The complete chloroplast genome sizes are 155,827 bp, 155,825 bp, and 155,792 bp in length, each including 86 Protein-Coding Genes (PCGs), 8 rRNA genes, and 38 tRNA genes. Phylogenetic analysis of chloroplast PCG sequences confirmed that the three color phenotypes are variants of P. kingianum, indicating that the white-flowered phenotype represents the ancestral trait. Comparative analysis of chloroplast genome structures among closely related species revealed no substantial differences in repeat composition or codon usage bias between the color phenotypes. The consistent IR boundary contraction/expansion patterns provided additional evidence for a highly conserved chloroplast genome structure. These distinct characteristics from other Polygonatum species substantiated that the three flower color phenotypes are phenotypic variations of P. kingianum. Furthermore, we identified hypervariable regions suitable for use as DNA barcodes to authenticate different flower-color phenotypes of P. kingianum and distinguish them from adulterant species.