Phylogenetic analysis of Uncaria species based on internal transcribed spacer (ITS) region and ITS2 secondary structure

Abstract

Context: The plant genus Uncaria (Rubiaceae), also known as Gouteng, is the source of an important traditional Chinese medicine. Misidentification and adulteration of Gouteng affect the safety and efficacy of the medication. Phylogenetic relationships among the species of this genus are unknown.Objective: The present study sought to detect the phylogenetic relationships based on internal transcribed spacer (ITS) region of all 12 species of Uncaria recorded in the Flora of China.Materials and methods: Accession of seven species of Uncaria served as reference samples. ITS region was used for polymerase chain reaction (PCR) amplification of the reference samples representing 39 specimens. Distance analysis, species discrimination, and secondary structure of ITS2 were used to assess the ability of ITS sequence in authenticating. The phylogenetic relationships were detected using three methods: Bayesian inference (BI), maximum likelihood (ML), and neighbor joining (NJ).Results: Five species of traditional Chinese medicine Gouteng were well resolved in molecular phylogenetic tree. Besides, Uncaria lancifolia Hutch. was closer to U. rhynchophylloides F.C. How and U. sessilifructus Roxb. was closer to U. laevigata Wall. within the tree. Further, we also found that ITS2 secondary structure can be a candidate tool in distinguishing two closely related species U. yunnanensis K.C.Hsia and U. lanosa Wall. For accurate identification of different species of Uncaria based on species-specific nucleotide sites, a consensus sequences database with all 12 species is established.Discussions and conclusions: The results are able to discriminate Uncaria species and illustrate the phylogenetic relationships, which are essential for the investigation of adulterants and misidentifications of Uncaria.

Comparison of matK and rbcL DNA barcodes for genetic classification of jewel orchid accessions in Vietnam

“…However; the same gene cannot be employed in plants, as it lacks sufficient variations due to low mutation rate [2]. For plants, other gene regions have been utilized as DNA barcodes, such as nuclear ribosomal internal transcribed space (ITS) [3,4], also rbcL, matK, atpF-atpH, psbK-psbI, and trnH-psbA [5][6][7].…”

Investigating Potential Inhibitory Effect of Uncaria tomentosa (Cat’s Claw) against the Main Protease 3CLpro of SARS‐CoV‐2 by Molecular Modeling

“…However, its popular use has been widely known worldwide, and analytical tests can be found in the United States Pharmacopeia and dosage forms have been authorized only as dietary supplements. Currently, there are about 34 species of Uncaria, with Uncaria tomentosa being the most common species [ 12 ].…”

DNA barcoding: an efficient technology to authenticate plant species of traditional Chinese medicine and recent advances

“…ITS2 could be used as an alternative mini-barcoding when a full-length ITS is not available and can correctly identify R. rosea. [ 43 ], and U. lanosa [ 42 ], among many other species. Currently, effective experimental methods have been developed to avoid fungal contaminants.…”

“…ITS2 can identify 92.7% of species correctly in more than 6600 samples obtained from 4800 species in 753 genera [16,26], such as Cynanchum auriculatum [35], Acanthopanacis [36], Dipsacales [37], Xueteng [38]. Besides, the secondary structures of ITS2 provided additional information that enhances the species' discrimination [39][40][41][42]. ITS2 could be used as an alternative mini-barcoding when a full-length ITS is not available and can correctly identify R. rosea.…”