Genetic diversity in two threatened species in Vietnam: Taxus chinensis and Taxus wallichiana

Vu, Dinh Duy; Bui, Thi Tuyet Xuan; Nguyen, Minh Tam; Vu, Dinh Giap; Nguyen, Mai; Bui, Van Thang; Huang, Xiaohua; Zhang, Yi

doi:10.1007/s11676-016-0323-1

Cited by 20 publications

(22 citation statements)

References 22 publications

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“…The levels of genetic variation of a species are mainly determined by ecological, demographic, and life history (Nevo et al, 1984). However, recent human-induced habitat fragmentation has had a severely adverse impact on genetic diversity, resulting in decreased population sizes (Martín et al, 2014), reduced effective population sizes (Ne) (Manoel et al, 2012), increased inbreeding (Vu et al, 2016) and the occurrence of strong spatial genetic structure (SGS; Sjölund and Jump, 2015), which can severely reduce within-population genetic diversity and adaptive ability under changing environmental conditions. Thus, understanding the levels of genetic diversity is crucial to developing practical and effective conservation strategies for endangered species.…”

Section: Introductionmentioning

confidence: 99%

“…In the genus Taxus, sexual formations are complex, including the exclusive monoecious T. canadensis (Wilson et al, 1996), pure dioecious T. wallichiana (Vu et al, 2016) and T. contorta (Poudel et al, 2014) and mixed T. brevifolia (Hogg et al, 1996) and T. baccata (Di Cosmo, 2005). Studies of genetic diversity have shown that many exclusive and mixed Taxus species have an especially high level of inbreeding, with FIS values of 0.226 to 0.472 (El-Kassaby and Yanchuk, 1994;Chung et al, 1999;Myking et al, 2009;Dubreuil et al, 2010;Zhang and Zhou, 2013;Poudel et al, 2014;Vu et al, 2016). T. yunnanensis has long been believed to a strictly dioecious tree; however, cosexuality has recently been confirmed in this species (Wang et al, 2008).…”

Section: Introductionmentioning

confidence: 99%

“…mairei from China (HE = 0.538; Zhang and Zhou, 2013).It is not clear why wind-pollinated plants such as T. yunnanensis exhibit such high inbreeding (mean FIS = 0.596/0.702) within populations. Indeed, six Taxus species have been shown to have particularly high levels of inbreeding to date, namely, T. baccata(FIS = 0.226/0.448;Myking et al, 2009;Dubreuil et al, 2010), T. chinensis(FIS = 0.250;Vu et al, 2016), T. wallichiana(FIS = 0.270/0.400; Zhang and Zhou, 2013; Vu et al, 2016), T. contorta (FIS = 0.418;Poudel et al, 2014), T. brevifolia (FIS = 0.472; El-Kassaby and Yanchuk, 1994) and T. cuspidata (FIS = 0.229;…”

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confidence: 99%

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Low genetic diversity in the endangeredTaxus yunnanensisfollowing a population bottleneck, a low effective population size and increased inbreeding

Miao

Zhang

2016

Silvae Genetica

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Taxus yunnanensis, which is an endangered tree that is considered valuable because it contains the effective natural anticancer metabolite taxol and heteropolysaccharides, has long suffered from severe habitat fragmentation. In this study, the levels of genetic diversity in two populations of 136 individuals were analyzed based on eleven polymorphic microsatellite loci. Our results suggested that these two populations were characterized by low genetic diversity (NE = 2.303/2.557; HO = 0.168/0.142; HE = 0.453/0.517), a population bottleneck, a low effective population size (Ne = 7/9), a high level of inbreeding (FIS = 0.596/0.702), and a weak, but significant spatial genetic structure (Sp = 0.001, b = −0.001*). Habitat fragmentation, seed shadow overlap and limited seed and pollen dispersal and potential selfing may have contributed to the observed gene tic structure. The results of the present study will enable development of practical conservation measures to effectively conserve the valuable genetic resources of this endangered plant.

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Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

mentioning

confidence: 99%

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Low genetic diversity in the endangeredTaxus yunnanensisfollowing a population bottleneck, a low effective population size and increased inbreeding

Miao

Zhang

2016

Silvae Genetica

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“…The H o and H e for all five populations, calculated from data from the 14 loci, ranged from 0.664–0.728 and 0.514–0.633 (data not shown); these values were higher than those found in T. jackii Chun ( H o = 0.5012, H e = 0.4830; Li, ), Taxus chinensis (Pilg.) Rehder ( H o = 0.107, H e = 0.121; Vu et al., ), and Taxus cuspidata Siebold & Zucc. ( H o = 0.263, H e = 0.028; Cheng et al., ).…”

Section: Methods and Resultsmentioning

confidence: 99%

Development of microsatellite markers for a Chinese endemic plant, Torreya yunnanensis (Taxaceae)

Wang

Cheng²,

Li³

et al. 2018

Appl Plant Sci

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Premise of the StudyMicrosatellite markers were developed in Torreya yunnanensis (Taxaceae) to investigate the genetic diversity, phylogeography, and population structure of the species.Methods and ResultsSixteen primer sets were identified using Illumina 2 × 100‐bp paired‐end sequencing and bioinformatic screening. Most primers also amplified in T. fargesii, T. grandis, T. jackii, and T. nucifera.ConclusionsThese results indicate the utility of these microsatellite markers in T. yunnanensis for future studies of molecular ecology as well as their applicability across the genus.

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“…As a functional molecular marker, SSRs generated from expressed sequence tags (EST-SSRs) can investigate the effects of environmental heterogeneity and local adaptation due to its tight linkage with functional genes controlling phenotype [20][21][22]. Up till now numbers of EST-SSRs developed and checked for polymorphism in many species, such as sweet potato [23], Sesamum indicum [24], radish [25], Cymbidium sinense [26], Chinese bayberry [27], Silver r [28], Salix, Populus, Eucalyptus [29]; Rosa roxburghii [30], Neottopteris nidus [16], Lacquar tree [31], Bread wheat [32], Proso Millet [33], Almond [34] and Ginseng [35]. Limited genomic resources have been developed for Panax species so far, e.g., P. vietnamensis var.…”

Section: Introductionmentioning

confidence: 99%

De novo assembly and transcriptome characterization of an endemic species of Vietnam, Panax vietnamensis Ha et Grushv., including the development of EST-SSR markers for population genetics

Shah

Pham

et al. 2020

Preprint

Self Cite

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Abstract Background: Understanding the genetic diversity in endangered species that occur in forest remnants is necessary to establish efficient strategies for the species conservation, restoration and management. Panax vietnamensis Ha et Grushv. is medicinally important, endemic and endangered species of Vietnam. However, genetic diversity and structure of population are unknown due to lack of efficient molecular markers. Results: In this study, we employed Illumina HiSeqTM 4000 sequencing to analyze the transcriptomes of P. vietnamensis (roots, leaves and stems). Raw reads total of 23,741,783 was obtained and then assembled, from which the generated unigenes were 89,271 (average length = 598.3191 nt). The 31,686 unigenes were annotated in different databases i.e. Gene Ontology, Kyoto Encyclopedia of Genes and Genomes, Nucleotide Collection (NR/NT) and Swiss-Prot for functional annotation. Further, 11,343 EST-SSRs were detected. From 7,774 primer pairs, 101 were selected for polymorphism validation, in which; 20 primer pairs were successfully amplified to DNA fragments and significant amounts of polymorphism was observed within population. The nine polymorphic microsatellite loci were used for population structure and diversity analyses. The obtained results revealed high levels of genetic diversity in populations, the average observed and expected heterozygosity were HO = 0.422 and HE = 0.479, respectively. During the Bottleneck analysis using TPM and SMM models (p < 0.01) shows that targeted population is significantly heterozygote deficient. This suggests sign of the bottleneck in all populations. Genetic differentiation between populations was moderate (FST = 0.133) and indicating slightly high level of gene flow (Nm = 1.63). Analysis of molecular variance (AMOVA) showed 63.17% of variation within individuals and 12.45% among populations. Our results shows two genetic clusters related to geographical distances. Conclusion: Our study will assist conservators in future conservation management, breeding, production and habitats restoration of the species.

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Genetic diversity in two threatened species in Vietnam: Taxus chinensis and Taxus wallichiana

Cited by 20 publications

References 22 publications

Low genetic diversity in the endangeredTaxus yunnanensisfollowing a population bottleneck, a low effective population size and increased inbreeding

Low genetic diversity in the endangeredTaxus yunnanensisfollowing a population bottleneck, a low effective population size and increased inbreeding

Development of microsatellite markers for a Chinese endemic plant, Torreya yunnanensis (Taxaceae)

De novo assembly and transcriptome characterization of an endemic species of Vietnam, Panax vietnamensis Ha et Grushv., including the development of EST-SSR markers for population genetics

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