Genetic diversity and structure of the endemic and endangered species Aristolochia delavayi growing along the Jinsha River

Aristolochia delavayi Franch. is an endangered species of the dry hot valleys of the Jinsha River, southwestern China. The genetic diversity and structure of the species and the occurrence of gene flow were investigated with eight inter-simple sequence repeat (ISSR) markers and four plastid loci (matK, trnL-trnT, rps4-trnT, and trnC-rpoB). The analysis of ISSR markers indicated that the genetic diversity of the species is relatively high (PPB = 84.71%). Similarly, a high gene diversity of HT = 0.833 was found based on the four plastid loci. It is possible that this species previously maintained a large effective population size and that the current relict distribution of the species is a result of large-scale fragmentation and habitat destruction. The origin of the species at approximately 3.407 million years ago and the ensuing intraspecific divergence are generally consistent with the history of two major glaciations in this region. Conservation measures are urgently needed to increase the genetic diversity and population size of this species through both in- and ex-situ action.

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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

10.21203/rs.2.18797/v4 ◽

2020 ◽

Author(s):

Duy Dinh Vu ◽

Syed Noor Muhammad Shah ◽

Mai Phuong Pham ◽

Van Thang Bui ◽

Minh Tam Nguyen ◽

...

Keyword(s):

Genetic Diversity ◽

Endangered Species ◽

De Novo ◽

Average Length ◽

Species Conservation ◽

Illumina Hiseq ◽

Bottleneck Analysis ◽

Genetic Diversity And Structure ◽

Geographical Distances ◽

High Level

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 and structure in fragmented populations of the endangered species Ranunculus cabrerensis (Ranunculaceae): implications for conservation

Biologia ◽

10.2478/s11756-012-0126-6 ◽

2013 ◽

Vol 68 (1) ◽

Cited By ~ 6

Author(s):

Eduardo Cires ◽

Candela Cuesta ◽

José Fernández Prieto

Keyword(s):

Genetic Diversity ◽

Endangered Species ◽

Conservation Strategies ◽

Aflp Analysis ◽

Issr Primer ◽

Bayesian Analyses ◽

Principal Coordinates ◽

Genetic Diversity And Structure ◽

Different Populations ◽

Genetic Structures

AbstractRanunculus cabrerensis is an endemic and endangered species of the Northwestern Iberian Peninsula. The molecular markers AFLP and ISSR were used to investigate the genetic diversity and population structure of four populations across its known distribution. Fifteen selective primer combinations of AFLP and seventeen ISSR primer combinations produced a total of 2830 and 103 unambiguously repeatable fragments respectively, of which 97.57 and 81.38% were polymorphic for both markers. The genetic diversity of R. cabrerensis at species level was high (H E = 0.294 by ISSR and H E = 0.191 by AFLP) and differentiation between sampled locations was also relatively high (G ST = 0.316 and 0.158 by ISSR and AFLP analysis respectively) compared to other studies of endangered and rare species using the same techniques. The analysis of molecular variance (AMOVA) indicated that the main genetic variation was within sampled locations (73% by AFLP; 52% by ISSR), even though the variation among locations was also significant. Principal Coordinates, NeighborNet and Bayesian analyses revealed a weak but significant relationship between the genetic structures of different populations in R. cabrerensis, with gene flow acting as a homogenizing force that prevents stronger differentiation of populations. Finally, suggestions for conservation strategies to preserve the genetic resources of this species are outlined.

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Genetic diversity and structure of Atta robusta (Hymenoptera, Formicidae, Attini), an endangered species endemic to the restinga ecoregion

Genetics and Molecular Biology ◽

10.1590/s1415-47572014000400015 ◽

2014 ◽

Vol 37 (3) ◽

pp. 581-586 ◽

Cited By ~ 2

Author(s):

Evelyze Pinheiro dos Reis ◽

Tânia Maria Fernandes Salomão ◽

Lucio Antonio de Oliveira Campos ◽

Mara Garcia Tavares

Keyword(s):

Genetic Diversity ◽

Endangered Species ◽

Genetic Diversity And Structure

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Genetic diversity of butternut (Juglans cinerea) and implications for conservation

Canadian Journal of Forest Research ◽

10.1139/x08-030 ◽

2008 ◽

Vol 38 (4) ◽

pp. 899-907 ◽

Cited By ~ 15

Author(s):

Amy Ross-Davis ◽

Michael Ostry ◽

Keith E. Woeste

Keyword(s):

Genetic Diversity ◽

Population Genetics ◽

North America ◽

Endangered Species ◽

Isolation By Distance ◽

Eastern North America ◽

Native Range ◽

Juglans Cinerea ◽

Threatened And Endangered Species ◽

Genetic Diversity And Structure

The management of threatened and endangered species can be improved by understanding their patterns of genetic diversity and structure. This paper presents the results of the first analysis of the population genetics of butternut ( Juglans cinerea L.) using nuclear microsatellites. Butternut once was an economically and ecologically valuable hardwood, but now its numbers are rapidly decreasing throughout its native range in eastern North America. By genotyping butternut trees (n = 157) from five populations at seven highly polymorphic loci, we determined that the remaining genetic diversity for the species is considerably higher than previously estimated (mean HE = 0.75). Populations were nearly genetically homogenous (FST = 0.025), with no evidence of isolation by distance. These results indicate that butternut retains a large amount of genetic diversity, and that it is not too late to implement strategies to conserve local butternut populations.

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