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Lonicerae Flos (LF) derived from the dried flower buds or opening flowers of four  Lonicera  plants ( Lonicera macranthoides ,  L. hypoglauca ,  L. confusa , and  L. fulvotnetosa ), is a popular traditional Chinese medicine. Because the four origin plants are very similar in morphology, it is difficult to control the quality of LF in actual production. Over the past decade, many reports have pointed out the differences among them, including the botanical characteristics and active ingredients. However, there is still a lack of rapid methods that can be applied to the identification of the four origins. In this study, comparative analysis of the four chloroplast genomes was performed, and they showed low diversity (Pi = 0.00267), three variation hotspots regions ( rbcL-accD ,  rps12-ndhF  and  rps12-trnN-trnG ) were identified as potentially molecular marker of highly informative. Meanwhile, the most obvious difference in SSR comparative analysis is reverse and complement repeats were only identified in  L. confusa  and  L. hypoglauca , respectively. Lastly, the phylogenetic tree showed that  L. confusa  is more closely related to  L. fulvotnetosa , while  L. macranthoides  is closer to  L. hypoglauca . This study systematically revealed the differences among the four chloroplast genomes, and it provides valuable genetic information for identifying the origin of LF.

Comparative Analysis of the Complete Chloroplast Genome Sequences of Four Origin Plants of Lonicerae Flos ( Lonicera ; Caprifoliaceae)