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

<b>Background/Objectives:</b><i>Illicium verum</i> Hook. f. and <i>Illicium difengpi</i> 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>I. verum</i> and <i>I. difengpi</i>. <b>Methods</b>: Here, the cp genomes of the two plants were sequenced and analyzed. <b>Results</b>: The cp genome sizes were 142,689 and 142,689 bp for <i>I. verum</i> and <i>I. difengpi</i>, 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>I. verum</i>) and 1.18-10.17% (<i>I. difengpi</i>) were found in the coding genes. There were also 104 and 96 SSRs as well as 26 and 25 long repeats identified in <i>I. verum</i> and <i>I. difengpi</i>, respectively, among which the most common were A/T base repeats. Both cp genomes had SSC/IRa junctions located in gene <i>ycf1-trnN.</i> The <i>ycf1</i> and <i>trnL-trnV-rps7</i> 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 <i>Illicium</i>. <b>Conclusions</b>: The comparative cp genomes of <i>I. verum</i> and <i>I. difengpi</i> are presented in this study, and this provides valuable phylogenetic information for subsequent molecular marker development and research of <i>I. verum</i> and <i>I. difengpi</i>.