Target Capture Reveals the Complex Origin of Vietnamese Ginseng

Abstract

The global market of the medicinal plant ginseng is worth billions of dollars. Many ginseng species are threatened in the wild and effective sustainable development initiatives are necessary to preserve biodiversity at species and genetic level whilst meeting the demand for medicinal produce. This is also the case of Panax vietnamensis Ha & Grushv., an endemic and threatened ginseng species in Vietnam that is locally cultivated at different scales and has been the object of national breeding programs. To investigate the genetic diversity within cultivated and wild populations of P. vietnamensis we captured 353 nuclear markers using the Angiosperm-353 probe set. Genetic diversity and population structure were evaluated for 319 individuals of Vietnamese ginseng across its area of distribution and from wild and a varying range of cultivated areas. In total, 319 individuals were sampled. After filtering, 1,181 SNPs were recovered. From the population statistics, we observe high genetic diversity and high genetic flow between populations. This is also supported by the STRUCTURE analysis. The intense gene flow between populations and very low genetic differentiation is observed regardless of the populations' wild or cultivated status. High levels of admixture from two ancestral populations exist in both wild and cultivated samples. The high gene flow between populations can be attributed to ancient and on-going practices of cultivation, which exist in a continuum from understorey, untended breeding to irrigated farm cultivation and to trade and exchange activities. These results highlight the importance of partnering with indigenous peoples and local communities and taking their knowledge into account for biodiversity conservation and sustainable development of plants of high cultural value.

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

“…Similarly, microfluidics-based methods offer tailored tests for the detection of target species at a potentially low cost ( Li et al, 2023 ). Genomic barcoding approaches, such as target capture sequencing and genome skimming, are increasing the species identification resolution of DNA-based methods, enabling the distinction at an unprecedented scale of closely related species and even populations ( Handy et al, 2021 ; Woudstra et al, 2021 ; Le et al, 2022 ; Manzanilla et al, 2022 ). Although many of these technologies are still at a proof-of-concept stage, it is challenging to predict which methods will find a role in routine quality control applications.…”

“…However, Woudstra et al (2021) designed an RNA-bait panel targeting 189 low-copy nuclear genes that allows for accurate molecular identification of species from the genus Aloe L. This is particularly useful for the conservation and sustainable use of Aloe -derived products, as many Aloe species are regulated by the Convention on International Trade of Endangered Species (CITES). Additionally, Le et al (2022) captured 353 nuclear markers using 319 individuals to evaluate the genetic diversity within cultivated and wild populations of Panax vietnamensis Ha and Grushv, an endemic and threatened ginseng species in Vietnam.…”

Calceolariaceae809: A bait set for targeted sequencing of nuclear loci

“…Although bait‐capture approaches are becoming more common in phylogenetics, the use of group‐specific, custom bait sets is still limited in plants. Indeed, the Angiosperms353 bait set has improved phylogenetic inference in many groups (e.g., Crowl et al, 2022 ; Le et al, 2022 ; Schmidt‐Lebuhn, 2022 ; Simões et al, 2022 ; Thureborn et al, 2022 ), although its ability to recover deep relationships in the angiosperms is counterproductive when the aim is to understand relationships at lower taxonomic levels (e.g., interspecific). In our case, the Angiosperms353 ML phylogenetic reconstruction recovered a similar topology to our bait set (Figure 4 ), but displayed many very short branches, especially in the already hard‐to‐resolve southern clade (clade I in Cosacov et al, 2009 ).…”

Suspension cell cultures of Panax vietnamensis as a biotechnological source of ginsenosides: growth, cytology, and ginsenoside profile assessment

“…In 2007, P. vietnamensis was listed in the Red Data Book of Vietnam ( Vu et al., 2020 ). Systematic studies on the sexual and vegetative propagation of Vietnamese ginseng are being conducted to restore its population and expand plantation cultivation potential in Vietnam ( Le et al., 2022 ). However, plantation cultivation of Vietnamese ginseng is associated with numerous difficulties due to the complex requirements of the species to the growth environment and a period of 5–7 years to achieve high commercial quality ( Trong et al., 2017 ).…”