Complete chloroplast genome sequence and characteristic analysis of Paeonia suffruticosa from the lower reaches of the Yangtze River basin

Paeonia suffruticosa cv. ‘Yu Luo Chun’ is an important representative of the peony groups from the Jiangnan region of China. However, little is known about the genetic basis of chloroplast genome phylogeny and the adaptive evolution of this group. In this study, high-throughput sequencing technology was used to sequence the complete chloroplast genome of leaves, and sequence assembly, annotation and feature analysis were performed by bioinformatics analysis methods. The results showed that the chloroplast genome of P. suffruticosa cv. ‘Yu Luo Chun’ exhibited a typical tetrad structure with a total length of 152,596 bp, including a large single-copy (LSC) region, a small single-copy (SSC) region, and two inverted repeats (IRs) whose lengths were 84,272 bp, 17,044 bp and 25,640 bp, respectively. A total of 126 genes were annotated, including 85 protein-coding genes, 37 tRNA genes and 4 rRNA genes. Bioinformatics analysis showed that a total of 71 simple sequence repeats (SSRs) were searched in the chloroplast genome, of which the numbers of mononucleotide, dinucleotide, trinucleotide and tetranucleotide repeat motifs were 47, 12, 7 and 5, respectively, and no pentanucleotide or hexanucleotide repeat motifs were found. The chloroplast genome prefers to end in A/T, among which leucine (Leu) is the most frequently used, while cysteine ​​(Cys) is the least frequently used. Highly differentiated regions, such as rpoC1, petB, rsp16, rps19, clpP, ccsA, ycf1, ndhF-trnL, ndhD-psaC and trnV-rps12, were identified as DNA barcodes and potential genetic markers for interspecies relationships. We compared the gene selection pressure and identified 5 genes, ndhF, petB, petD, rpoA and ycf2 that were positively selected, and these genes have important contributions to the adaptive evolution. The chloroplast genome sequences of 18 species, including P. suffruticosa cv. ‘Yu Luo Chun’, were clustered by the nearest neighbour combination method and the maximum likelihood method. Both methods gave the same result and indicated that this cultivar has a relatively close kinship with P. qiui and P. rockii. The results provide important references for species identification, genetic diversity analysis and systematic taxonomic research between P. suffruticosa cv. ‘Yu Luo Chun’ and other Paeonia species.