Application of High Throughput Sequencing in the authentication and quality control of herbal material and products

Herbal material and products (HMPs) have gained worldwide popularity in the past decades. Yet the efficacy and safety of HMPs are frequently compromised by economically motivated adulteration, species substitution, and mislabelling. Conventional authentication methods, relying on morphology and chemical profiling, often fail short when dealing with complex multi-ingredient mixtures or trace contaminants. DNA-based methods have been widely adopted by various pharmacopeia, and the rapid development of high throughput sequencing technology has shown promising identifying power in related fields. This review examines the transformative application of High-Throughput Sequencing (HTS) in the authentication and quality control of herbal material and product, by exploring the advanced HTS techniques, including short-and long-read amplicon metabarcoding, shotgun metabarcoding, genome skimming, superbarcoding and target capture. These approaches offer unprecedented resolution, enabling simultaneous, multi-kingdom detection of prescribed species, adulterants, and contaminants, even in highly processed preparations. That said, HTS has challenges such as DNA degradation, extraction biases, and limitations in quantitative accuracy, integrating these genomic tools with orthogonal chemical analyses provides a rigorous, complementary framework. The transition toward multi-omics integration, portable sequencing applications, and artificial intelligence place HTS as a cornerstone for the future of authentication and quality control.