Comparative analysis of the chloroplast genome of Paeonia suffruticosa ‘Cun Song Ying’ reveals plastid characteristics and phylogenetic relationships

Chloroplast genomes provide valuable insights into plant evolution, phylogeny, and molecular breeding. Here, we present the first complete chloroplast genome of Paeonia suffruticosa ‘Cun Song Ying’. Using high-throughput sequencing combined with multiple bioinformatics approaches, we comprehensively characterized its chloroplast genome and compared it with those of closely related taxa. The chloroplast genome of ‘Cun Song Ying’ is 152,704 bp in length and exhibits the typical quadripartite structure, comprising a large single-copy region (LSC), a small single-copy region (SSC), and two inverted repeat regions (IRa and IRb). A total of 138 genes were annotated, including 4 pseudogenes and 134 functional genes, which consist of 87 protein-coding genes, 39 tRNAs, and 8 rRNAs. Phylogenetic analysis revealed that ‘Cun Song Ying’ shares the closest relationship with P. suffruticosa ‘Luo Yang Hong’. These findings provide new insights into the evolutionary history of peony plastids, and the identified highly variable regions may serve as potential DNA barcodes for cultivar identification.