Comparative analysis of the complete chloroplast genome of Pueraria provides insights for species identification, phylogenetic relationships, and taxonomy.

backgroundPueraria is an edible and medicinal raw material, which is of great value to the pharmaceutical and food industries. Nonetheless, due to morphological diversity and complex domestication history, the classification of Pueraria plants is ambiguous. As the varieties on the market are mixed, the species are difficult to distinguish, and their morphological characteristics are similar to the physical and chemical properties. It is difficult to accurately identify them by traditional identification methods. Chloroplast (cp) genomes are widely used in species identification and phylogenetic studies to achieve accurate identification of medicinal plants, and can also provide more reference information for phylogenetic studies. Based on interspecific and intraspecific sampling, the cp genomes of eight species or varieties of Pueraria plants were examined in this study.

resultsThe study unveiled that the cp genome size varied from 151,555 to 153,668 base pairs (bp), with the total GC content ranging from 35.4 to 37.0%. Moreover, it was discerned that the cp genome contained between 128 and 135 genes. Comparative analysis indicated that the highest number of Simple Sequence Repeats (SSRs) was identified in P. montana and P. alopecuroides, with a preponderance of these SSRs being rich in Adenine (A) and Thymine (T) nucleotides. Complete comparison and sliding window analysis of the cp genome established that the non-coding region exhibited greater sequence differences than the coding region, and that the large single copy (LSC) region demonstrated higher nucleotide polymorphism levels. Fourteen highly variable loci such as rpoB,ycf1,rbcL,trnF-GAA-trnL,psbC-psbD, and ycf4-cemA were detected as potential molecular markers for Pueraria species identification. Moreover, the phylogenetic tree demonstrated that other Pueraria species had the most distant relationship with Haymondia wallichii and Toxicopueraria peduncularis, thereby offering fresh perspectives into the species classification of Pueraria. The molecular clock analysis results indicate that the divergence time of Pueraria may occur at ∼6.46 Ma. It is speculated that the cold climate may be the cause of Pueraria species diversity and promote the radiation of the genus.

conclusionThis research provides theoretical backing and serves as a reference point for the identification and taxonomical classification of Pueraria species. The findings will prove beneficial in future studies on the preservation of medicinal resources, phylogenetic relationships, and genetic engineering of Pueraria plants.