Strategies for molecular authentication of herbal products: from experimental design to data analysis

Abstract

Molecular herbal authentication has gained worldwide popularity in the past decade. DNA-based methods, including DNA barcoding and species-specific amplification, have been adopted for herbal identification by various pharmacopoeias. Development of next-generating sequencing (NGS) drastically increased the throughput of sequencing process and has sped up sequence collection and assembly of organelle genomes, making more and more reference sequences/genomes available. NGS allows simultaneous sequencing of multiple reads, opening up the opportunity of identifying multiple species from one sample in one go. Two major experimental approaches have been applied in recent publications of identification of herbal products by NGS, the PCR-dependent DNA metabarcoding and PCR-free genome skimming/shotgun metagenomics. This review provides a brief introduction of the use of DNA metabarcoding and genome skimming/shotgun metagenomics in authentication of herbal products and discusses some important considerations in experimental design for botanical identification by NGS, with a specific focus on quality control, reference sequence database and different taxon assignment programs. The potential of quantification or abundance estimation by NGS is discussed and new scientific findings that could potentially interfere with accurate taxon assignment and/or quantification is presented.

Horizon scan of DNA-based methods for quality control and monitoring of herbal preparations

“…The application of DNA barcoding has been a significant breakthrough for both the research community and industry, enabling it to address a range of questions that were previously impossible to answer. Standardized DNA barcoding protocols have been proposed for the identification of plant material by Pharmacopeias around the world, including the Chinese, United States, Japanese, and British Pharmacopoeias ( Howard et al, 2009 ; Kreuzer et al, 2019 ; Ha et al, 2022 ; Wu and Shaw, 2022 ). The utility of DNA barcoding to detect adulteration has been shown in studies on herbal products derived from Ginkgo biloba L. ( Little, 2014a ), Actaea racemosa L. ( Baker et al, 2012 ), and species belonging to the genera Senna and Cassia ( Seethapathy et al, 2014 ), among others ( Ghorbani et al, 2015 ; Hart et al, 2016 ).…”

“…herbarium specimen and the nuclear genome sequence of 80-year-old fungi ( Staats et al, 2013 ), and recovered rDNA and plastid genome sequences of 80-year-old herbarium specimen using low concentrations of degraded material ( Zeng et al, 2018 ). It has also been used in herbal product authentication to overcome the limitations of standard DNA barcoding and metabarcoding ( Wu and Shaw, 2022 ). For instance, ( Handy et al, 2021 ), compared the performance of DNA metabarcoding, genome skimming, and HPLC-UV analysis to authenticate 20 commercially available dietary supplements containing Echinacea .…”

DNA metabarcoding using newrbcLandITS2metabarcodes collectively enhance detection efficiency of medicinal plants in single and polyherbal formulations

“…Nowadays, various pharmacopoeia is advocating DNA based methods such as DNA barcoding and species-specific PCR assay to authenticate herbal raw material as DNA is more stable, unaffected by the external factors, and present in almost all plant tissues invariably 3 . In addition, the DNA based results are independent of seasonal variations, age of the plant, which in case of chemical marker based methods vary significantly 4 .…”

Flower Species Ingredient Verification Using Orthogonal Molecular Methods

“…Molecular methods for botanical identi cation include the use of both DNA-based methods and analysis of phytochemicals present within botanical ingredients. DNA-based tools have been used for botanical ingredient identi cation to verify species ingredients on labels and unwanted adulterant species [49,50,51]. Targeted DNA methods have been validated and utilized within the food, herbal, and supplement industries [52].…”