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

Abstract

Background: Xi Junecry (Pinellia ternata), 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. Methods: 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. Results: 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: ndhE-ndhG, trnN-GUU-ndhF, trnS-GCU-trnG-UCC, atpB-rbcL, psaI, accD-ycf4, psbE-petL, psaC-ndhE, and psbI-trnG-UCC. Positive selection sites were detected in the accD and rbcL genes. Phylogenetic analysis clustered the six Xi Junecry samples into a distinct clade, separating them from other regional Pinellia samples. Conclusions: 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.

Keywords: Pinellia ternata (Xi Junecry); chloroplast genome; high variable region; nucleotide polymorphisms.

Figure 1

Chloroplast genome repeat analysis in Xi Junecry: (A) number of different types of SSR loci in the assembled green genome; (B) distribution of SSRs in the assembled chloroplast genome. Note: the sample names such as CL are the same as those in Table 1.

Figure 2

Sliding window analysis of Xi Junecry chloroplast genome.

Figure 3

Visualization of the whole sequence alignment of six Xi Junecry chloroplast genomes.

Figure 4

Phylogenetic tree based on whole chloroplast genome sequence (with only one inverted repeat region). Notes. Pinellia ternate I: CL; P. ternate II: GD; P. ternate III: PD; P. ternate IV: PW; P. ternate V: ZB; P. ternate VI: ZT.