Intraspecific Chloroplast Genome Genetic Polymorphism of Pinellia ternata (Xi Junecry) and Its Revelation of a Single Origin in Phylogeny

<b>Background</b>: Xi Junecry (<i>Pinellia ternata</i>), a perennial herb of the Araceae family, is indigenous to Xinxian County, Henan Province, China, and is regarded as a premium variety among similar medicinal materials. However, the lack of comprehensive genetic information on Xi Junecry germplasm resources has constrained the cultivation and identification of high-quality varieties. <b>Methods</b>: In this study, six chloroplast genomes of Xi Junecry were assembled and annotated using high-throughput sequencing. Subsequently, comparative analyses were conducted, and a phylogenetic tree was constructed. <b>Results</b>: The six Xi Junecry chloroplast genome lengths ranged from 157,456 to 158,406 bp, and the GC content was between 36.0% and 36.2%. A total of 265 single nucleotide polymorphism sites were identified across the six genomes, with a whole-genome nucleotide diversity (Pi) value of 0.00084. Among the four genomic regions, the small single-copy region exhibited the highest Pi, followed by the large single-copy region, while the inverted repeat region showed the lowest. Nucleotide polymorphism in coding regions was significantly lower than in non-coding regions. Nine hypervariable regions were identified, as follows: <i>ndhE-ndhG</i>, <i>trnN-GUU-ndhF, trnS-GCU-trnG-UCC</i>, <i>atpB-rbcL</i>, <i>psaI</i>, <i>accD-ycf4</i>, <i>psbE-petL</i>, <i>psaC-ndhE</i>, and <i>psbI-trnG-UCC</i>. Positive selection sites were detected in the <i>accD</i> and <i>rbcL</i> genes. Phylogenetic analysis clustered the six Xi Junecry samples into a distinct clade, separating them from other regional <i>Pinellia</i> samples. <b>Conclusions</b>: These findings elucidate the genetic variation levels in Xi Junecry and provide high-variability loci for population history inference, genetic diversity assessment, species domestication studies, and new cultivar development.