Testing and using complete plastomes for authentication of medicinal Polygonatum species (Asparagaceae)

Wang, Shuying; Zhou, Nian; Shi, Naixing; Zhang, Guangfei; Liu, Hai-Yang; Guo, Xinfeng; Ji, Yunheng

doi:10.1016/j.indcrop.2023.116557

Cited by 5 publications

(1 citation statement)

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“…Compared with single or multiple sequence regions generated by Sanger sequencing, either complete plastomes or nrDNA arrays possess far more variable loci; therefore, the application of both datasets in plant species discrimination is considered to have great potential for improving resolution [ 21 , 23 , 35 , 40 – 43 ]. Consistent with this theoretical expectation, empirical studies have shown that although the application of genome skimming is not yet robust enough to distinguish all species, especially in evolutionarily young and complex plant taxa, it can substantially improve the efficacy of species discrimination in most of the studied taxa [ 38 , 41 , 44 – 52 ]. Better yet, previous studies have shown that even using trace and highly degraded genomic DNA extracted from processed plant materials to build shotgun libraries, complete plastomes and nrDNA arrays can be recovered by application of high-throughput sequencing technologies [ 35 , 37 , 38 ], and the use of genome skimming has shown desirable performance in accurate and sensitive identification of species in mixed samples [ 53 , 54 ].…”

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confidence: 95%

Genome skimming as an efficient tool for authenticating commercial products of the pharmaceutically important Paris yunnanensis (Melanthiaceae)

et al. 2023

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Background Paris yunnanensis (Melanthiaceae) is a traditional Chinese medicinal plant of significant pharmaceutical importance. Due to previous taxonomic confusion, a congeneric species, Paris liiana, has been mistaken for P. yunnanensis and cultivated on a large scale, leading to the mixing of commercial products (i.e., seedlings and processed rhizomes) of P. yunnanensis with those of P. liiana. This may have adverse effects on quality control in the standardization of P. yunnanensis productions. As the lack of PCR amplifiable genomic DNA within processed rhizomes is an intractable obstacle to the authentication of P. yunnanensis products using PCR-based diagnostic tools, this study aimed to develop a PCR-free method to authenticate commercial P. yunnanensis products, by applying genome skimming to generate complete plastomes and nrDNA arrays for use as the molecular tags. Results Based on a dense intraspecies sampling of P. liiana and P. yunnanensis, the robustness of the proposed authentication systems was evaluated by phylogenetic inferences and experimental authentication of commercial seedling and processed rhizome samples. The results indicate that the genetic criteria of both complete plastomes and nrDNA arrays were consistent with the species boundaries to achieve accurate discrimination of P. yunnanensis and P. liinna. Owing to its desirable accuracy and sensitivity, genome skimming can serve as an effective and sensitive tool for monitoring and controlling the trade of P. yunnanensis products. Conclusion This study provides a new way to solve the long-standing problem of the molecular authentication of processed plant products due to the lack of PCR amplifiable genomic DNA. The proposed authentication system will support quality control in the standardization of P. yunnanensis products in cultivation and drug production. This study also provides molecular evidence to clarify the long-standing taxonomic confusion regarding the species delimitation of P. yunnanensis, which will contribute to the rational exploration and conservation of the species.

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