Comparative analysis of 17 complete chloroplast genomes reveals intraspecific variation and relationships among Pseudostellaria heterophylla (Miq.) Pax populations

Pseudostellaria heterophylla (Miq.) Pax is a well-known medicinal and ecologically important plant. Effectively distinguishing its different genetic resources is essential for its breeding. Plant chloroplast genomes can provide much more information than traditional molecular markers and provide higher-resolution genetic analyses to distinguish closely related planting materials. Here, seventeen P. heterophylla samples from Anhui, Fujian, Guizhou, Hebei, Hunan, Jiangsu, and Shandong provinces were collected, and a genome skimming strategy was employed to obtain their chloroplast genomes. The P. heterophylla chloroplast genomes ranged from 149,356 bp to 149,592 bp in length, and a total of 111 unique genes were annotated, including 77 protein-coding genes, 30 tRNA genes, and four rRNA genes. Codon usage analysis showed that leucine had the highest frequency, while UUU (encoding phenylalanine) and UGC (encoding cysteine) were identified as the most and least frequently used codons, respectively. A total of 75–84 SSRs, 16–21 short tandem repeats, and 27–32 long repeat structures were identified in these chloroplast genomes. Then, four primer pairs were revealed for identifying SSR polymorphisms. Palindromes are the dominant type, accounting for an average of 47.86% of all long repeat sequences. Gene orders were highly collinear, and IR regions were highly conserved. Genome alignment indicated that there were four intergenic regions (psaI-ycf4, ycf3-trnS, ndhC-trnV, and ndhI-ndhG) and three coding genes (ndhJ, ycf1, and rpl20) that were highly variable among different P. heterophylla samples. Moreover, 10 SNP/MNP sites with high polymorphism were selected for further study. Phylogenetic analysis showed that populations of Chinese were clustered into a monophyletic group, in which the non-flowering variety formed a separate subclade with high statistical support. In this study, the comparative analysis of complete chloroplast genomes revealed intraspecific variations in P. heterophylla and further supported the idea that chloroplast genomes could elucidate relatedness among closely related cultivation materials.