The screening and identification of DNA barcode sequences for Rehmannia

Abstract

In this study, ITS, ITS2, matK, rbcL and psbA-trnH in Rehmannia were successfully amplified and sequenced, but some ITS sequences need to be proofread according to ITS2 sequences. Compared with rbcL, matK and psbA-trnH, ITS and ITS2 had higher mutation rate and more information sites, and ITS2 had higher interspecific diversity and lower intraspecific variation in Rehmannia, but the interspecific genetic variation of rbcL and matK was lower. Furthermore, the obvious barcoding gap was found in psbA-trnH or ITS2 + psbA-trnH, and the overlap between interspecific and intraspecific variation of ITS, ITS2 or matK was less. In addition, the phylogenetic tree based on ITS or ITS2 indicated that R. glutinosa, R. chingii or R. henryi with obvious monophyly could be successfully identified, but R. piasezkii and R. elata were clustered into one branch, R. solanifolia could not be distinguished from R. glutinosa, and R. chingii was closer to R. henryi. In phylogenetic tree based on psbA-trnH or ITS2 + psbA-trnH, cultivars and wild varieties of R. glutinosa could be distinguished, were clearly separated from other Rehmannia species, and cultivars or wild varieties of R. glutinosa could be also distinguished by matK. Taken together, ITS2 has great potential in systematic study and species identification of Rehmannia, the combination of ITS2 and psbA-trnH might be the most suitable DNA barcode for Rehmannia species.

Phytochemical Analysis and Evaluation of Antioxidant and Biological Activities of Extracts from Three Clauseneae Plants in Northern Thailand

“…A combination of both markers, mat K + rbc L, could help to discriminate between a maximum number of species. However, a number of researchers have used the integration of the DNA barcode to classify and identify species, while several different combinations of DNA barcodes have been effectively put forward for different plants [ 20 ]. To attain a maximum discrimination rate among closely related species, a combination of Internal Transcribed Spacers (ITS + mat K + rbc L) has been suggested by Li et al [ 22 ].…”

“…DNA barcoding, a modern method for the rapid identification of any species, is considered as a molecular and bioinformatics tool for species differentiation, identification and discovery of new species at molecular systematic level [ 16 ]. In terms of barcoding of vascular plants, it was mostly focused on markers of chloroplast genes, several markers were assessed and with time most commonly applied combinations are rbc L, mat K, trn H -psb A, with a nuclear internal transcribed spacer 2 (ITS2) established [ 17 , 18 , 19 , 20 ].…”

Phylogenetic analysis of six different species of Saraca L. (Fabaceae, Caesalpinioideae) based on chloroplast matK gene

“…DNA barcoding, particularly via applying different chloroplast genes like the matK sequence, can help determine genetic divergence (Duan et al 2019) and protect endangered plant species (Gogoi and Bahu 2018). Different species of Saraca are threatened due to overexploitation and reductions in the gene pool.…”

The utility of DNA barcodes to confirm the identification of palm collections in botanical gardens

“…[27,43]). Due to the high degree of universality of its primers, its short sequence length and high capacity for species resolution, ITS2 has been widely used in plant barcoding [44,45], especially in metabarcoding in recent years [46]; e.g., for pollen provenance determination [47] and for environmental DNA identification [48]. Taking into account the high rate of species resolution and the cost-effectiveness associated with the relatively high sequence recovery rates, we agree with Jeanson et al [5] that ITS2 should be to supplement the two 'core' markers in palms, which has been shown to have consistent results across a range of families and genera (e.g., [49]).…”