Development of a Specific Mini-Barcode From Plastome and its Application for Qualitative and Quantitative Identification of Processed Herbal Products Using DNA Metabarcoding Technique: A Case Study on Senna

Abstract

Herbal products play an important role globally in the pharmaceutical and healthcare industries. However, some specific groups of herbal products are easily adulterated by confused materials on the market, which seriously reduces the products’ quality. Universal conventional DNA barcodes would function poorly since the processed herbal products generally suffer from varying degrees of DNA degradation and DNA mixing during processing or manufacturing. For quality control purposes, an accurate and effective method should be provided for species identification of these herbal products. Here, we provided a strategy of developing the specific mini-barcode using Senna as an example, and by coupling with the metabarcoding technique, it realized the qualitative and quantitative identification of processed herbal products. The plastomes of Senna obtusifolia (L.) H.S.Irwin & Barneby and Senna occidentalis (L.) Link were newly assembled, and the hypervariable coding-regions were identified by comparing their genomes. Then, the specific mini-barcodes were developed based on the identified hypervariable regions. Finally, we applied the DNA metabarcoding technique to the developed mini-barcodes. Results showed that the lengths of plastomes of S. obtusifolia and S. occidentalis were 162,426 and 159,993 bp, respectively. Four hypervariable coding-regions ycf1, rpl23, petL, and matK were identified. Two specific mini-barcodes were successfully developed from matK, and the mini-barcode of primer 647F-847R was proved to be able to qualitatively and quantitatively identify these two processed Senna seeds. Overall, our study established a valuable way to develop the specific mini-barcode, which may provide a new idea for the quality control of processed herbal products.

Development of Mini-Barcode Based on Chloroplast Genome and Its Application in Metabarcoding Molecular Identification of Chinese Medicinal Material Radix Paeoniae Rubra (Chishao)

“…The nature of the chloroplast genome, including its small size, conserved structure and gene content, moderate evolutionary rate and variations among gene loci, has rendered this genome more useful in molecular evolutionary analyses and phylogenetic reconstruction than mitochondrial and nuclear genomes ( Drouin et al, 2008 ; Daniell et al, 2016 ; Park et al, 2018 ; Biju et al, 2019 ; Li et al, 2020 ). In previous research, Yu et al (2020) had developed specific DNA mini-barcode from chloroplast genomes, and integrated them with DNA metabarcoding technology to differentiate Senna medicinal materials qualitatively and quantitatively.…”

The complete chloroplast genome ofSenna alata(L.) Roxb., an important medicinal plant from the Philippines

“… 2020 ) and S. obtusifolia with 162,426 bp (Yu et al. 2020 ). The chloroplast genome of S. alata comprised of 123 genes coding for 37 tRNAs, 8 rRNAs and 78 mRNAs.…”

Evolutionary history of genus Coptis and its dynamic changes in the potential suitable distribution area

“…Notably, mini barcodes may facilitate discrimination of DNA degradation materials, such as herbarium specimens, processed medicinal plant, or even fossil material. Moreover, this strategy of developing taxon-specific barcodes by comparing plastid genome sequences has also been applied in other medicinal plant taxa, including Panax , Senna , and Paeonia ( Dong et al., 2014 ; Yu X. et al., 2020 ; Yang et al., 2022 ). Collectively, these two hotspots should be promising mini-barcodes for Coptis species identification in future applications.…”