Chloroplast genome analysis and phylogenetic position of Polygonatum sinopubescens and comparison with related species

The genus Polygonatum (Asparagaceae) comprises perennial herbaceous plants with significant economic and medicinal value. In this study, we analyzed the complete chloroplast (cp) genome of Polygonatum sinopubescens and compared it with closely related species. The primary objective was to elucidate structural variations, species divergence, and phylogenetic relationships among taxa. The cp genome of P. sinopubescens exhibits the typical quadripartite structure, consisting of a large single-copy (LSC) region, a small single-copy (SSC) region, and a pair of inverted repeats (IRs), with a total sequence length of 155,307 bp and a GC content of 37.68%. The present analysis revealed a high degree of consistency in gene order and GC content between P. sinopubescens and other Polygonatum species. A total of 112 genes were annotated, including 78 protein-coding genes, 30 tRNA genes, and 4 rRNA genes. The genome contained 67 simple sequence repeats (SSRs), and codon usage was biased toward codons ending in A/T; among the 30 codons with RSCU > 1, 93.3% ended with A/T. Nucleotide polymorphism analysis identified nine highly variable regions, and selection pressure analysis revealed that only ndhA, ycf2, accD, and rbcL genes were under positive selection (Ka/Ks > 1), which was observed in only a subset of species. Phylogenetic analyses indicated that Polygonatum is a monophyletic group that can be divided into three major clades. P. sinopubescens was placed in sect. Polygonatum and was most closely related to P. filipes. This study provides a comprehensive characterization of the cp genome of P. sinopubescens and clarifies its phylogenetic placement, offering important references for species identification, evolutionary studies, and phylogenetic research within Polygonatum.