Target capture reveals the complex origin of Vietnamese ginseng (Panax vietnamensis) Hien Thi Thu LE1,2*, Linh Nhat NGUYEN1, Hang Le Bich PHAM1, Hao Thi My LE3, Toan Duc LUONG3, Hue Thi Thu HUYNH1,2, Van Tuong NGUYEN4, Hai Van NONG1,2, Irene TEIXIDOR-TONEU5, Hugo J. DE BOER5, Vincent MANZANILLA6* 1Institute of Genome Research, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay, Hanoi, 10000, Viet Nam 2Graduate University of Science and Technology, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay, Hanoi, 10000, Viet Nam 3Soils and Fertilizers Research Institute, Vietnam Academy of Agricultural Sciences, 10 Duc Thang, Bac Tu Liem, Hanoi, 10000, Vietnam 4Institute of Biotechnology, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay, Hanoi, 10000, Viet Nam 5Natural History Museum, University of Oslo, 0562 Oslo, Norway 6Baseclear BV, 2333 Leiden, Netherlands. *Corresponding authors: Hien Thi Thu LE (hienlethu@igr.ac.vn, tel. +84-24-37918014) and Vincent MANZANILLA (vincent.manzanilla@gmail.com, tel. +47-41209706) 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 programmes. 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, 1181 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.