A Comparative Analysis and Phylogenetic Relationship of the Chloroplast Genome Sequences of Illicium verum and Illicium difengpi

Background/Objectives: Illicium verum Hook. f. and Illicium difengpi K. I. B.et K. I. M. are two important medicinal plants which grow in the mountainous areas of Guangxi, China. Their similar morphological characteristics frequently lead to their misidentification. Chloroplast genome (cp)-based barcode technology has been used to effectively identify two closely related species; however, at present, there is no systematic comparative study of the cp genome sequences between I. verum and I. difengpi. Methods: Here, the cp genomes of the two plants were sequenced and analyzed. Results: The cp genome sizes were 142,689 and 142,689 bp for I. verum and I. difengpi, respectively. Each of the cp genomes annotated 122 genes, with 79 protein coding genes, 8 ribosomal RNA genes, and 35 transfer RNA genes. Amino acid frequencies of 1.17–10.19% (I. verum) and 1.18–10.17% (I. difengpi) were found in the coding genes. There were also 104 and 96 SSRs as well as 26 and 25 long repeats identified in I. verum and I. difengpi, respectively, among which the most common were A/T base repeats. Both cp genomes had SSC/IRa junctions located in gene ycf1-trnN. The ycf1 and trnL-trnV-rps7 genes were positioned at the IRb/SSC and LSC/IR boundaries, respectively. A phylogenetic relationship was constructed and the two species were fully nested within the genus Illicium. Conclusions: The comparative cp genomes of I. verum and I. difengpi are presented in this study, and this provides valuable phylogenetic information for subsequent molecular marker development and research of I. verum and I. difengpi.