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Regional and estimated genetic structure for K = 2 for 72 populations of G. pentaphyllum. (a) Individual assignment to two clusters for all 72 populations was visualized as pie charts. Each population was partitioned into several colored parts proportionally to its membership in a given cluster; colored rings around the pie charts represented the ploidy of each population (gray: diploid; light blue: tetraploid; orange: hexaploid; purple: octaploid). (b) STRUCTURE plot presented for K = 2. Each vertical bar represents a population and its assignment proportion into one of two (colored) population clusters (K). The arrows represented the migration paths
Source publication
Abstract Gynostemma pentaphyllum, a member of family Cucurbitaceae, is a perennial creeping herb used as a traditional medicinal plant in China. In this study, six polymorphic nSSR and four EST‐SSR primers were used to genotype 1,020 individuals in 72 wild populations of G. pentaphyllum. The genetic diversity and population structure were investiga...
Citations
... Microsatellite markers evolve relatively quickly and are biparental and codominant inheritance, reflecting the impacts of pollen flow on genetic diversity patterns [41,42]. The cpDNA and SSRs markers have been successfully employed to detect genetic diversities in numerous plant species [43][44][45][46][47][48][49]. Nevertheless, few studies use both markers together to focus on the population genetics of medicinal plants. ...
Background
The sustainable supply of medicinal plants is important, and cultivating and domesticating them has been suggested as an optimal strategy. However, this can lead to a loss of genetic diversity. Tripterygium wilfordii Hook. f. is a medicinal plant commonly used in traditional Chinese medicine, but its wild populations are dwindling due to excessive harvesting. To protect the species and meet the increasing demand, it is urgent to cultivate it on a large scale. However, distinguishing between T. wilfordii and T. hypoglaucum, two similar species with different medicinal properties, is challenging. Therefore, it is crucial to understand the genetic diversity and population structure of these species for their sustainable utilization.
Results
In this study, we investigated the genetic diversity and population structure of the two traditional medicinal semiwoody vines plant species, Tripterygium wilfordii and T. hypoglaucum, including wild and cultivated populations using chloroplast DNA (cpDNA) sequences and microsatellite loci. Our results indicated that the two species maintain a high level of genetic divergence, indicating possible genetic bases for the different contents of bioactive compounds of the two species. T. wilfordii showed lower genetic diversity and less subdivided population structures of both markers than T. hypoglaucum. The potential factors in shaping these interesting differences might be differentiated pollen-to-seed migration rates, interbreeding, and history of population divergence. Analyses of cpDNA and microsatellite loci supported that the two species are genetically distinct entities. In addition, a significant reduction of genetic diversity was observed for cultivated populations of the two species, which mainly resulted from the small initial population size and propagated vegetative practice during their cultivation.
Conclusion
Our findings indicate significant genetic divergence between T. wilfordii and T. hypoglaucum. The genetic diversity and population structure analyses provide important insights into the sustainable cultivation and utilization of these medicinal plants. Accurate identification and conservation efforts are necessary for both species to ensure the safety and effectiveness of crude drug use. Our study also highlighted the importance of combined analyses of different DNA markers in addressing population genetics of medicinal plants because of the contrasts of inheritance and rates of gene flow. Large-scale cultivation programs should consider preserving genetic diversity to enhance the long-term sustainability of T. wilfordii and T. hypoglaucum. Our study proposed that some populations showed higher genetic diversity and distinctness, which can be considered with priority for conservation and as the sources for future breeding and genetic improvement.
... The predicted probability of presence of G. pentaphyllum responds positively to Bio2 (Fig. 4g) and negatively to Bio1 (Fig. 4h and i), therefore areas with increasing annual mean diurnal range but decreasing annual mean temperature increases the suitability of G. pentaphyllum for such areas. This coincides with the models of Zhang et al. (2019) predicting that temperature is the primary factor influencing the distribution of G. pentaphyllum. The Fuzzy Matter Element (FME) model of Zhao et al. (2017) predicted that the optimal value of Bio1 for Chinese strains of G. pentaphyllum is 17 °C. ...
... Such conditions suggest that G. pentaphyllum thrives in relatively cold areas which, in a tropical archipelago such as the Philippines, are typical of mountainous areas. This is consistent with the earlier SDMs predicting that G. pentaphyllum grows most appropriately, and possibly even originating from, the mountainous areas of China (Zhang et al. 2018(Zhang et al. , 2019. Also, the FME model by Zhao et al. (2017) predicted that an altitude of 200-2000 m was most appropriate for the growth of G. pentaphyllum. ...
Climate change shifts the distribution of socioeconomically important medicinal species such as Ganoderma lucidum and Gynostemma pentaphyllum, renowned as immortality mushroom and herb, respectively. To predict their ecological niche and potential distribution in the Philippines, species distribution modeling (SDM) was performed using two algorithms under three climate change scenarios: current, and future Shared Socioeconomic Pathways (SSPs) 1–2.6 and 3–7.0 of the EC-Earth3-Veg-LR Earth System Model for 2081–2100. Maximum entropy (MaxEnt) and Genetic Algorithm for Rule Set Production (GARP) yielded acceptable mean Area Under the ROC (Receiver Operating Characteristic) curve (AUC) scores (0.677–0.806). MaxEnt models predict that, under the current scenario, G. lucidum is distributed in low-altitude, open forests with high temperature and precipitation seasonality in mainland Luzon. Meanwhile, G. pentaphyllum is distributed in annually cold and highly diurnal high-altitude mountains across the whole archipelago. Under both future scenarios, based on percent change of very highly suitable areas, G. lucidum is predicted to decrease in suitability (–2.67 to –5.30%) and undergo upward range reduction, while G. pentaphyllum is predicted to increase in suitability (+ 6.75 to + 25.61%) and undergo downward range expansion. However, these migration trends are not evident in GARP models due to its overpredictive nature, mainly due to the use of categorical predictors. Hence, for its conservative predictions, MaxEnt is recommended for presence-only (PO) modeling. These models establish baseline information for local threat assessment and conservation planning for both ‘immortality’ flora. This is the first report of medicinal macrofungus and herb utilizing SDM in the Philippines.
... In this method, which requires a long time and effort; the cytological procedures for the preparation and staining of chromosomes vary according to the plant species and if plants are in an in vivo or in vitro conditions(Song et al. 2007;Mohamed and Refaei, 2004;Abdollahi et al. 2016;Dong et al. 2016). TheSang (2002) technique has been applied for chromosome counts.Nevertheless, chromosomes of several species in this family are too small and hard to determine even if by using a microscope of high power(Zhang et al. 2019a). ...
... Researches on genetic diversity and population structure of medicinal plants are the premise and fundamental issues for the protection and utilization of medicinal plant germplasm resources. The protection of medicinal plant germplasm resources is to protect its genetic diversity and evolutionary potentials [9,10]. Although F. hirta have been successfully cultivated in some areas, to some extent, which also relieved the pressure on nature resources, long term cultivation and directional selection of this species may also cause the loss of genetic diversity, further lose their ability of resisting the epidemic of pests and diseases [11,12]. ...
Background
Wuzhimaotao (Radix Fici Hirtae) originates from the dry root of Ficus hirta (Moraceae), which is widely known as a medical and edible plant distributed in South China. As the increasing demand for Wuzhimaotao, the wild F. hirta has been extremely reduced during the past years. It is urgent to protect and rationally develop the wild resources of F. hirta for its sustainable utilization. However, a lack of genetic background of F. hirta makes it difficult to plan conservation and breeding strategies for this medical plant. In the present study, a total of 414 accessions of F. hirta from 7 provinces in southern China were evaluated for the population genetics using 9 polymorphic SSR markers.
Results
A mean of 17.1 alleles per locus was observed. The expected heterozygosity ( H e) varied from 0.142 to 0.861 (mean = 0.706) in nine SSR loci. High genetic diversity ( H e = 0.706, ranged from 0.613 to 0.755) and low genetic differentiation among populations ( G’ ST = 0.147) were revealed at population level. In addition, analysis of molecular variance (AMOVA) indicated that the principal molecular variance existed within populations (96.2%) was significantly higher than that among populations (3.8%). Meanwhile, the three kinds of clustering methods analysis (STRUCTURE, PCoA and UPGMA) suggested that the sampled populations were clustered into two main genetic groups (K = 2). Mantel test showed a significant correlation between geographic and genetic distance among populations ( R ² = 0.281, P < 0.001). Pollen flow, seed flow and/or geographical barriers might be the main factors that formed the current genetic patterns of F. hirta populations.
Conclusions
This is a comprehensive study of genetic diversity and population structure of F. hirta in southern China. We revealed the high genetic diversity and low population differentiation in this medicinal plant and clarified the causes of its current genetic patterns. Our study will provide novel insights into the exploitation and conservation strategies for F. hirta .
... This suggests that polyploid populations likely originated polyphyletically from their neighboring diploid populations and coexisted with their diploid parents within a certain geographic range. A similar inference has also been found in previous studies of Galax urceolata [34] and G. pentaphyllum [35]. More definitive assessment as to whether polyploidization in A. chinensis arose once or multiple times will require other data such as high-throughput DNA sequence methods. ...
Understanding genetic diversity and structure in natural populations and their suitable habitat response to environmental changes is critical for the protection and utilization of germplasm resources. We evaluated the genetic diversity and structure of 24 A. chinensis populations using simple sequence repeat (SSR) molecular markers. The potential suitable distribution of tetraploid A. chinensis estimated under the current climate and predicted for the future climate was generated with ecological niche modeling (ENM). The results indicated that the polyploid populations of A.chinensis have high levels of genetic diversity and that there are distinct eastern and western genetic clusters. The population structure of A. chinensis can be explained by an isolation-by-distance model. The results also revealed that potentially suitable areas of tetraploids will likely be gradually lost and the habitat will likely be increasingly fragmented in the future. This study provides an extensive overview of tetraploid A. chinensis across its distribution range, contributing to a better understanding of its germplasm resources. These results can also provide the scientific basis for the protection and sustainable utilization of kiwifruit wild resources.
... The heterozygosity values observed (Ho) were much lower than the expected heterozygosity (He). This phenomenon, constituting a heterozygosity deficit, is related to genetic drift and nonrandom mating between individuals of the populations, related in turn to migration [71]. However, it is today understood that S. cerevisiae mostly reproduces through budding or intra-ascus mating (both reducing the heterozygosity level of the population) in most natural environments. ...
Vitis vinifera L. ssp. sylvestris (Gmelin) Hegi is recognized as the dioecious parental generation of today’s cultivars. Climatic change and the arrival of pathogens and pests in Europe led it to be included on the International Union for Conservation of Nature (IUCN) Red List of Threatened Species in 1997. The present work focused on the study of culturable yeast occurrence and diversity of grape berries collected from wild vines. Sampling was performed in 29 locations of Azerbaijan, Georgia, Italy, Romania, and Spain. In total, 3431 yeast colonies were isolated and identified as belonging to 49 species, including Saccharomyces cerevisiae, by 26S rDNA D1/D2 domains and ITS region sequencing. Isolates of S. cerevisiae were also analyzed by SSR–PCR obtaining 185 different genotypes. Classical ecology indices were used to obtain the richness (S), the biodiversity (H’), and the dominance (D) of the species studied. This study highlights the biodiversity potential of natural environments that still represent a fascinating source of solutions to common problems in winemaking.
... The more abundant the genetic variation of a species is, the more adaptable it is. Thus, it is necessary to study the genetic diversity of a species to understand its biological properties [43]. All previous studies on this species revealed a relatively high level of genetic diversity [22]. ...
Cunninghamia lanceolate (Lambert.) Hooker is one of the main fast-growing timber forest species in southern China which has a long history of cultivation and spreads across 28 provinces, cities, and regions. Recently, a variant of fir was discovered in the Xiaoxi National Nature Reserve in Hunan Province. The heartwood is hard as iron and its ratio is more than 80%, with the especial character of anti-corruption. It is a natural germplasm resource, called Iron-heart Cunninghamia lanceolate. Study on it is still in the stage of data accumulation. In this paper, we studied it from three points as follows: (1) Plus tree selection and construction of germplasm resources nursery. (2) Study on cone and seed quality. (3) Genetic structure analysis of natural population. The research of Iron-heart Cunninghamia lanceolate lays a theoretical foundation for the protection, development, and utilization of the black-heart wood germplasm resources of Iron-heart Cunninghamia lanceolate in the future.
... Makino (2n ¼ 2Â ¼ 22), a traditional Chinese medicinal herb of the Cucurbitaceae family, is widely distributed in Southeast Asia, including China, Korea, and Japan. 1 Gynostemma pentaphyllum was first recorded in Jiuhuang Bencao (Materia Medica for the Relief of Famine), which was compiled by Zhu Su in AD 1406 to prepare for natural disasters and to extend traditional Chinese medicine ( Supplementary Fig. S1). Gypenosides, a class of triterpenoid saponin compounds with dammarane-type structure, are effective chemical ingredients in G. pentaphyllum. ...
Gynostemma pentaphyllum (Thunb.) Makino is an economically valuable medicinal plant belonging to the Cucurbitaceae family that produces the bioactive compound gypenoside. Despite several transcriptomes having been generated for G. pentaphyllum, a reference genome is still unavailable, which has limited the understanding of the gypenoside biosynthesis and regulatory mechanism. Here, we report a high-quality G. pentaphyllum genome with a total length of 582 Mb comprising 1,232 contigs and a scaffold N50 of 50.78 Mb. The G. pentaphyllum genome comprised 59.14% repetitive sequences and 25,285 protein-coding genes. Comparative genome analysis revealed that G. pentaphyllum was related to Siraitia grosvenorii, with an estimated divergence time dating to the Paleogene (∼48 million years ago). By combining transcriptome data from seven tissues, we reconstructed the gypenoside biosynthetic pathway and potential regulatory network using tissue-specific gene co-expression network analysis. Four UDP-glucuronosyltransferases (UGTs), belonging to the UGT85 subfamily and forming a gene cluster, were involved in catalyzing glycosylation in leaf-specific gypenoside biosynthesis. Furthermore, candidate biosynthetic genes and transcription factors involved in the gypenoside regulatory network were identified. The genetic information obtained in this study provides insights into gypenoside biosynthesis and lays the foundation for further exploration of the gypenoside regulatory mechanism.
... important role in plant diversification and adaptation to novel environments [14]. Although the wide recognition of the prevalence of polyploidy and accumulative cytological evidence for recent whole-genome duplication(s) in many plant groups [15,16], studies on the phylogeography of polyploid species in these two hotspots in China [17][18][19] are few relative to those in other hotspots in the world (e.g. North America and Alps in Central Europe). ...
Background
Plant phylogeographic studies of species in subtropical China have mainly focused on rare and endangered species, whereas few studies have been conducted on taxa with relatively wide distribution, especially polyploid species. We investigated the cytotype and haplotype distribution pattern of the Actinidia chinensis complex, a widespread geographically woody liana with variable ploidy in subtropical China comprising two varieties, with three chloroplast fragments DNA ( ndh F- rpl 132, rps 16- trn Q and trn E- trn T). Macroevolutionary, microevolutionary and niche modeling tools were also combined to disentangle the origin and the demographic history of the species or cytotypes.
Results
The ploidy levels of 3338 individuals from 128 populations sampled throughout the species distribution range were estimated with flow cytometry. The widespread cytotypes were diploids followed by tetraploids and hexaploids, whereas triploids and octoploids occurred in a few populations. Thirty-one chloroplast haplotypes were detected. The genetic diversity and genetic structure were found to be high between varieties (or ploidy races) chinensis and deliciosa . Our results revealed that these two varieties inhabit significantly different climatic niche spaces. Ecological niche models (ENMs) indicate that all varieties’ ranges contracted during the Last Inter Glacial (LIG), and expanded eastward or northward during the Last Glacial Maximum (LGM).
Conclusions
Pliocene and Plio-Pleistocene climatic fluctuations and vicariance appear to have played key roles in shaping current population structure and historical demography in the A. chinensis complex. The polyploidization process also appears to have played an important role in the historical demography of the complex through improving their adaptability to environmental changes.
... Historical and ecological factors have left complex imprints on the genetic structure and demographic history of extant species (e.g., Petit et al., 2002;Chen et al., 2008;Zhang et al., 2019). These factors include geographical and/or climatic processes, such as the uplift of the mountains, morphological reconstruction, and climatic oscillations associated with ice ages. ...
... It is possible that these mountains provided a diverse range of thermal, hydric, and edaphic conditions, as well as complex and mesic habitats for Q. fabri during glacial periods in the Pleistocene. Thus, mountains are likely to have served as important refugia for Q. fabri in a similar manner to many other plants, according to previous studies (e.g., Gavin et al., 2014;Tian et al., 2015;Zhang et al., 2019). ...
Oak trees (Quercus L.) are important models for estimating abiotic impacts on the population structure and demography of long life span tree species. In this study, we generated genetic data for 17 nuclear microsatellite loci in 29 natural populations of Quercus fabri to estimate the population genetic structure. We also integrated approximate Bayesian computation (ABC) and ecological niche analysis to infer the population differentiation processes and demographic history of this oak species. The genetic analyses indicated two genetic clusters across the 29 populations collected, where most approximately corresponded to the intraspecific differentiation among populations from western and eastern China, whereas admixed populations were mainly found in central mountains of China. The best model obtained from hierarchical ABC simulations suggested that the initial intraspecific divergence of Q. fabri potentially occurred during the late Pliocene (ca. 3.99 Ma) to form the two genetic clusters, and the admixed population group might have been generated by genetic admixture of the two differentiated groups at ca. 53.76 ka. Ecological analyses demonstrated clear differentiation among the Q. fabri population structures, and association estimations also indicated significant correlations between geography and climate with the genetic variation in this oak species. Our results suggest abiotic influences, including past climatic changes and ecological factors, might have affected the genetic differentiation and demographic history of Q. fabri in subtropical China.
