Plastome sequencing for accurate and effective authentication of Polygonatum kingianum (Asparagaceae)

Guo, Xinfeng; Shi, Naixing; Xie, Pingxuan; Zhang, Guangfei; Liu, Haiyang; Ji, Yunheng

doi:10.1016/j.indcrop.2022.115056

Cited by 10 publications

(11 citation statements)

References 65 publications

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“…This study describes a protocol for rapidly obtaining a primary species delimitation scheme. In some cases, plastome data contributes to discovering cryptic diversity or sorting out problematic taxonomic treatments [ 24 , 74 , 75 ], and have formed the primary basis of formal taxonomic revisions [ 25 , 76 ]. In other cases, an integrative strategy including plastome data has been applied for delimiting species.…”

Section: Discussionmentioning

confidence: 99%

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Species delimitation of tea plants (Camellia sect. Thea) based on super-barcodes

Jiang,

Yang,

Folk

et al. 2024

BMC Plant Biol

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Background The era of high throughput sequencing offers new paths to identifying species boundaries that are complementary to traditional morphology-based delimitations. De novo species delimitation using traditional or DNA super-barcodes serve as efficient approaches to recognizing putative species (molecular operational taxonomic units, MOTUs). Tea plants (Camellia sect. Thea) form a group of morphologically similar species with significant economic value, providing the raw material for tea, which is the most popular nonalcoholic caffeine-containing beverage in the world. Taxonomic challenges have arisen from vague species boundaries in this group. Results Based on the most comprehensive sampling of C. sect. Thea by far (165 individuals of 39 morphospecies), we applied three de novo species delimitation methods (ASAP, PTP, and mPTP) using plastome data to provide an independent evaluation of morphology-based species boundaries in tea plants. Comparing MOTU partitions with morphospecies, we particularly tested the congruence of MOTUs resulting from different methods. We recognized 28 consensus MOTUs within C. sect. Thea, while tentatively suggesting that 11 morphospecies be discarded. Ten of the 28 consensus MOTUs were uncovered as morphospecies complexes in need of further study integrating other evidence. Our results also showed a strong imbalance among the analyzed MOTUs in terms of the number of molecular diagnostic characters. Conclusion This study serves as a solid step forward for recognizing the underlying species boundaries of tea plants, providing a needed evidence-based framework for the utilization and conservation of this economically important plant group.

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Section: Discussionmentioning

confidence: 99%

“…For example, molecular delimitation in Orychophragmus (Brassicaceae) highlighted the application of plastomes to jointly examining species boundaries and establishing phylogenetic relationships [ 24 ]. Another case based on Polygonatum kingianum demonstrated the ability to delimit species on the basis of the plastid genome [ 25 ].…”

Section: Introductionmentioning

confidence: 99%

Species delimitation of tea plants (Camellia sect. Thea) based on super-barcodes

Jiang,

Yang,

Folk

et al. 2024

BMC Plant Biol

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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 ].…”

Section: Introductionmentioning

confidence: 94%

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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“…Such a database is convenient for the management, traceability and resource investigation of TCM (Wongchai et al, 2022). Big data analysis driven by AI is based on medicinal materials samples and covers many aspects, including authenticity identification, origin tracking and quality prediction (Guo et al, 2022). The application of AI technology in TCM varieties, origin distribution, and cultivation techniques has achieved remarkable results, which provides strong technical support for the standardization of TCM cultivation.…”

Section: Tcm Cultivationmentioning

confidence: 99%

Integrating artificial intelligence into the modernization of traditional Chinese medicine industry: a review

Zhou,

Shen,

Hou

2024

Front. Pharmacol.

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Traditional Chinese medicine (TCM) is the practical experience and summary of the Chinese nation for thousands of years. It shows great potential in treating various chronic diseases, complex diseases and major infectious diseases, and has gradually attracted the attention of people all over the world. However, due to the complexity of prescription and action mechanism of TCM, the development of TCM industry is still in a relatively conservative stage. With the rise of artificial intelligence technology in various fields, many scholars began to apply artificial intelligence technology to traditional Chinese medicine industry and made remarkable progress. This paper comprehensively summarizes the important role of artificial intelligence in the development of traditional Chinese medicine industry from various aspects, including new drug discovery, data mining, quality standardization and industry technology of traditional Chinese medicine. The limitations of artificial intelligence in these applications are also emphasized, including the lack of pharmacological research, database quality problems and the challenges brought by human-computer interaction. Nevertheless, the development of artificial intelligence has brought new opportunities and innovations to the modernization of traditional Chinese medicine. Integrating artificial intelligence technology into the comprehensive application of Chinese medicine industry is expected to overcome the major problems faced by traditional Chinese medicine industry and further promote the modernization of the whole traditional Chinese medicine industry.

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Plastome sequencing for accurate and effective authentication of Polygonatum kingianum (Asparagaceae)

Cited by 10 publications

References 65 publications

Species delimitation of tea plants (Camellia sect. Thea) based on super-barcodes

Species delimitation of tea plants (Camellia sect. Thea) based on super-barcodes

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

Integrating artificial intelligence into the modernization of traditional Chinese medicine industry: a review

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