AUTHOR=Dai Jiangpeng , Liu Qiaozhen , Xu Xingyuan , Tan Zhijie , Lin Yuexia , Gao Xiaoxia , Zhu Shuang 

TITLE=Comparative and phylogenetic analysis of the complete chloroplast genomes of Uncaria (Rubiaceae) species

JOURNAL=Frontiers in Plant Science

VOLUME=14

YEAR=2023

URL=https://www.frontiersin.org/journals/plant-science/articles/10.3389/fpls.2023.1271689

DOI=10.3389/fpls.2023.1271689

ISSN=1664-462X

ABSTRACT=<p>The genus <italic>Uncaria</italic> is famous for its high medicinal value. However, the high morphological similarities and unclear interspecific genetic relationships have posed challenges to the classification and identification of <italic>Uncaria</italic> species. Here, we newly sequenced six chloroplast genomes of <italic>Uncaria</italic> species: <italic>U. hirsuta</italic>, <italic>U. rhynchophylla</italic>, <italic>U. rhynchophylloides</italic>, <italic>U. homomalla</italic>, <italic>U. sinensis</italic>, and <italic>U. lancifolia</italic>. Comparisons among the chloroplast genomes of <italic>Uncaria</italic> species showed their conservation in structure, gene content, and order. Ten highly variable loci could be potentially used as specific molecular markers in the identification of <italic>Uncaria</italic> species. The third position of codons tended to use A/U base, and natural selection contributed more to the formation of codon usage bias in comparison to mutation pressure. Four genes (<italic>rbc</italic>L, <italic>ndh</italic>F, <italic>rps</italic>8, and <italic>ycf</italic>2) were detected to be subjected to positive selection. Phylogenetic analysis showed that the genus <italic>Uncaria</italic> was a monophyletic group, belonging to the tribe Naucleeae. Moreover, <italic>U. sinensis</italic> was not a variant of <italic>U. rhynchophylla</italic>. <italic>U. rhynchophylloides</italic> and <italic>U. rhynchophylla</italic> were not the same species. The results of the comparative and phylogenetic analysis provide valuable references for further research studies of classification, identification, breeding improvement, and phylogenetic relationships in <italic>Uncaria</italic> species.</p>