Living on the Edge: Various Modes of Persistence at the Range Margins of Some Far Eastern Species

Artyukova, E. V.; Козыренко, М. М.; Koren, O. G.; Kholina, A. B.; Nakonechnaya, O. V.; Zhuravlev, Yuri N.

doi:10.5772/35032

Cited by 6 publications

(6 citation statements)

References 45 publications

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“…In this study, only wild ginseng was investigated. Furthermore, the populations studied inhabit the northeastern margin of the former range of ginseng, which may be one of the reasons for the observed reduction in the level of genetic variability [40]. Similar values of SSR genetic diversity were observed in two related species, P. notoginseng (H e = 0.350, [43]), and P. vietnamensis (H e = 0.550, [44]).…”

Section: Genetic Diversitysupporting

confidence: 56%

“…The populations of P. ginseng growing on Primorsky Territory of Russia are characterized by a lower level of allozymes and dominant markers variation than most species with restricted ranges [40]. Our earlier studies demonstrated low levels of genetic variability in P. ginseng, as detected by allozymes (Р = 7.6%, Н е = 0.022), RAPD (Р = 4.0%, Н е = 0.013) and ISSR (P = 9.3%, H e = 0.014) [17] [19] [21].…”

Section: Genetic Diversitymentioning

confidence: 99%

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Microsatellite Analysis of <i>Panax ginseng</i> Natural Populations in Russia

Реунова¹,

Koren²,

Музарок³

et al. 2014

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Panax ginseng C.A. Meyer is an endangered species in Russia. To restore this species, effective protective measures, including the reintroduction into favorable habitats, must be worked out considering the specificity of genetic structure of ginseng populations. One hundred and thirtynine P. ginseng plants were collected from the forests of nine administrative areas of Primorsky Territory of Russia and transferred to a collection nursery for further investigation. Microsatellite markers were used to study the genetic diversity and the genetic structure of ginseng populations. For populations studied with SSR, the number of observed alleles was ranging from 15 to 25, allelic richness from 1.83 to 3.04, polymorphic loci from 62.5% to 87.7%, observed heterozygosity from 0.410 to 0.512 (an average of 0.453) and expected heterozygosity from 0.304 to 0.479, with an average of 0.393. The values of the inbreeding coefficient within populations (Fis) ranged from −0.447 to 0.056, and their average value was −0.296. Genetic differentiation among populations was significant (F st = 0.115) but an isolation-by-distance pattern was not detected. UPGMA and MStree confirmed the presence of genetic structure within P. ginseng and visualized genetic relationships of populations with similar pattern. STRUCTURE analysis revealed the genetic admixture between different ginseng populations. It was established with SSR markers that P. ginseng still preserves substantial genetic resources although all populations are largely exhausted. Because ginseng populations are significantly differentiated all of them should be restored. Considering the admixture of ginseng populations it would be advisable to apply the individual assignment test to verify the content of indigenous populations and to identify the "true" population plants to serve as stock material for reintroduction.

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Section: Genetic Diversitysupporting

confidence: 56%

Section: Genetic Diversitymentioning

confidence: 99%

Microsatellite Analysis of <i>Panax ginseng</i> Natural Populations in Russia

Реунова¹,

Koren²,

Музарок³

et al. 2014

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“…The genetic diversity degree in many plants can be linked with the numbers of loci and populations [31,69], the geographical range size [70] and genetic exchange [71]. In the current research, the nine SSR markers showed a high degree of genetic diversity in P. vietnamensis populations and expected heterozygosity (H O = 0.422 and H E = 0.479) compared to some Panax species, such as P. stipuleanatus [50], P. ginseng [72,73] However, our results are in line with studies of Reunova et al [46] on P. ginseng, the natural species of Russia (H O = 0.453 and H E = 0.393), Liu et al [74] on P. notoginseng (H E = 0.350) and Reunova et al [75] on P. vietnamensis (H E = 0.55) using microsatellite markers. High levels of genetic diversity in three P. vietnamensis populations, TN, DT and KT indicated that this species is predominantly outcrossed.…”

Section: Discussionmentioning

confidence: 77%

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

BMC Plant Biol

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Background: Understanding the genetic diversity in endangered species that occur inforest 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 HiSeq™ 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 7774 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 H O = 0.422 and H E = 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 (F ST = 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.

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“…The genetic diversity degree in many plants can be linked with the numbers of loci and populations [32,71], the geographical range size [72] and genetic exchange [73]. In the current research, the nine SSR markers showed a high degree of genetic diversity in P. vietnamensis populations and expected heterozygosity (H O = 0.422 and H E = 0.479) compared to some Panax species, such as P. stipuleanatus [51], P. ginseng [74,75] However, our results are in line with studies of Reunova et al [47] on P. ginseng, the natural species of Russia (H O = 0.453 and H E = 0.393), Liu et al [76] on P. notoginseng (H E = 0.350) and Reunova et al [77] on P. vietnamensis (H E = 0.55) using microsatellite markers. Positive…”

Section: Discussionmentioning

confidence: 77%

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

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Background: Understanding the genetic diversity in threatened 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 is unknown due to lack of efficient molecular markers.Results: In this study, we employed Illumina HiSeq TM 4000 sequencing to analyze the transcriptomes of P. vietnamensis (roots, leaves and stems). A total of 23,741,783 raw reads were obtained and assembled, from which, 89,271 unigenes with an average length of 598.3191 nt were generated. During functional annotation, 31,686 unigenes were annotated in Gene Ontology categories, Kyoto Encyclopedia of Genes and Genomes pathways, Swiss-Prot database, and Nucleotide Collection (NR/NT) database. In addition, 11,343 expressed sequence tag-simple sequence repeat (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 to analyze genetic diversity and structure of the natural populations. The obtained results revealed that the shows high levels of genetic diversity in populations, the average observed and expected heterozygosity were H O = 0.422 and H E = 0.479. During the Bottleneck analysis using TPM and SMM models (p < 0.01) shows that targeted population is significantly heterozygote deficient. This suggests sign of bottleneck in all populations. Genetic differentiation among populations was moderate (F ST = 0.133) and indicating limited gene flow (Nm = 1.63). Analysis of molecular variance (AMOVA) showed 63.17% of variation within individuals and 12.45% among populations. These results showed a moderate genetic structure of P. vietnamensis. STRUCTURE analysis and the unweighted pair-group method with arithmetic means (UPGMA) tree revealed strong genetic structure and two genetic clusters related to geographical distances, as well. Conclusion: Our study will assist conservators in future conservation management, breeding, production and habitats restoration of the species.

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Living on the Edge: Various Modes of Persistence at the Range Margins of Some Far Eastern Species

Cited by 6 publications

References 45 publications

Microsatellite Analysis of <i>Panax ginseng</i> Natural Populations in Russia

Microsatellite Analysis of <i>Panax ginseng</i> Natural Populations in Russia

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

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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Living on the Edge: Various Modes of Persistence at the Range Margins of Some Far Eastern Species

Cited by 6 publications

References 45 publications

Microsatellite Analysis of &lt;i&gt;Panax ginseng&lt;/i&gt; Natural Populations in Russia

Microsatellite Analysis of &lt;i&gt;Panax ginseng&lt;/i&gt; Natural Populations in Russia

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

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

Contact Info

Product

Resources

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Microsatellite Analysis of <i>Panax ginseng</i> Natural Populations in Russia

Microsatellite Analysis of <i>Panax ginseng</i> Natural Populations in Russia