Browse
Submit Data
Databases
API
Help

Dataset Information

29 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Isolation and characterization of 20 polymorphic microsatellite markers for Juglans mandshurica (Juglandaceae).

ABSTRACT: UNLABELLED: PREMISE OF THE STUDY:Fifty microsatellite loci were developed for the endangered species Juglans mandshurica to investigate its genetic diversity and population structure. • METHODS AND RESULTS:In all, 50 microsatellite markers were isolated from J. mandshurica, using the Fast Isolation by AFLP of Sequences COntaining repeats (FIASCO) protocol. Twenty of these polymorphic markers were assessed in samples collected from 98 individuals among five populations in northeastern China. Across all of the J. mandshurica samples, the number of alleles per locus ranged from one to 17. • CONCLUSIONS:These new microsatellite loci will be useful for conservation genetics studies of J. mandshurica.

SUBMITTER: Chen CM

PROVIDER: S-EPMC4103126 | biostudies-literature | 2013 Jul

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Isolation and characterization of 20 polymorphic microsatellite markers for Juglans mandshurica (Juglandaceae).

Chen Chang-Mei CM Han Shi-Jie SJ Yuan Shu-Sheng SS Wang Chun-Jing CJ Yu Jing-Hua JH

Applications in plant sciences 20130628 7

<h4>Unlabelled</h4><h4>Premise of the study</h4>Fifty microsatellite loci were developed for the endangered species Juglans mandshurica to investigate its genetic diversity and population structure. •<h4>Methods and results</h4>In all, 50 microsatellite markers were isolated from J. mandshurica, using the Fast Isolation by AFLP of Sequences COntaining repeats (FIASCO) protocol. Twenty of these polymorphic markers were assessed in samples collected from 98 individuals among five populations in no ...[more]

PMID: 25202563

Similar Datasets

Isolation and characterization of microsatellite loci from <i>Pterocarya stenoptera</i> (Juglandaceae).

Project description:Premise of the studyMicrosatellite markers of Pterocarya stenoptera (Juglandaceae) were developed for future studies on the population genetic diversity and spatial genetic structure of the species.Methods and resultsBased on Illumina sequencing of the transcriptome of P. stenoptera, a total of 2452 microsatellites were identified from 83,674 assembled unigenes. One hundred microsatellites were randomly selected to design amplification primer pairs. Of these, 15 were successfully amplified and displayed polymorphism. For these markers, the number of alleles per locus and population ranged from one to six. The levels of observed and expected heterozygosity varied from 0.000 to 1.000 and 0.000 to 0.718, respectively. Furthermore, all of the 15 loci were successfully cross-amplified in another congeneric species (P. hupehensis) and were demonstrated to be polymorphic.ConclusionsThe microsatellite loci described here can be used for future population genetic and landscape genetic studies on P. stenoptera.

| S-EPMC6303151 | biostudies-literature

Isolation and characterization of polymorphic microsatellite markers for the masked palm civet (Paguma larvata).

Project description:The masked palm civet (Paguma larvata) has been suspected to be the host of a SARS-like CoV virus that causes severe acute respiratory syndrome in humans. In China, the palm civet lives wild and is farmed, but even though the species is a potential carrier of the virus, its geographic distribution and genetic diversity have never been studied. We report the isolation and characterization of six polymorphic microsatellite markers for P. larvata. To characterize each locus, two farmed masked palm civet populations from Shanxi and Guangxi provinces in China were genotyped. The number of alleles per locus ranged from 3 to 15, and the observed heterozygosity for these populations was 47.1 and 68.7%, respectively.

| S-EPMC7087744 | biostudies-literature

Isolation and Characterization of 11 Polymorphic Microsatellite Markers Developed for Orthops palus (Heteroptera: Miridae).

Project description:Miridae (Hemiptera: Heteroptera: Cimicomorpha), or plant bugs, are one of the most diverse and species-rich families of insects. Most of them are phytophagous, but some are insect predators and used for biocontrol. Among this family, the mango bug, Orthops palus (Taylor 1947), is one of the most important pest of mango in Reunion Island. We developed 11 polymorphic microsatellite loci to study the population genetics of this pest species. The microsatellite markers were characterized by genotyping 78 field-collected insects sampled at different localities in Reunion Island. The number of alleles per locus ranged from 1 to 13 and heterozygosity levels ranged between 0.40 and 0.94. Several loci were not at Hardy-Weinberg equilibrium for the tested populations. These markers are the first to be developed for a species of the genus Orthops.

| S-EPMC4776738 | biostudies-literature

Isolation and characterization of polymorphic microsatellite markers from the Chinese medicinal herb Atractylodes macrocephala (Asteraceae).

Project description:Atractylodes macrocephala Koidz. (Asteraceae) is an economically important Chinese medicinal herb. In this study, 15 polymorphic microsatellite markers were developed from A. macrocephala using the compound microsatellite marker technique. Levels of polymorphism within the 15 markers were assessed using 83 individuals from two wild and two cultivated populations in China. The number of alleles per locus ranged from 2 to 20, with an average of 9.9 alleles. Observed and expected heterozygosities ranged from 0.083 to 1.000 and from 0.097 to 0.938, respectively. These markers will be valuable for germplasm classi?cation and identi?cation, as well as for assessing the genetic diversity and spatial genetic structure among wild and cultivated populations of A. macrocephala.

| S-EPMC3546677 | biostudies-literature

Development and characterization of 20 polymorphic microsatellite markers for the white-bellied pangolin Phataginus tricuspis (Mammalia, Pholidota).

Project description:Pangolins, or scaly anteaters, have recently been flagshiped as one of the most illegally traded mammals, and as a corollary, as potential intermediate hosts at the origin of the COVID-19 pandemic. In order to improve the traceability of their trade, we developed 20 polymorphic microsatellite loci for the white-bellied pangolin (Phataginus tricuspis), the species most frequently found on African bushmeat markets. We genotyped 24 white-bellied pangolins from the Douala market, Cameroon, originating from the Ebo forest c. 75 km north-east of Douala. The number of alleles per locus ranged from 4 to 12 (mean?=?6.95), and mean observed and expected heterozygosities were 0.592 (0.208-0.875) and 0.671 (0.469-0.836), respectively. Genetic diversity was higher than that cross-estimated from microsatellite loci developed for other species of pangolins. Two loci deviated from Hardy-Weinberg equilibrium and two loci showed linkage disequilibrium. Genetic variance (PCoA) was increased with the addition of 13 pangolins of unknown origin, possibly suggesting that the Douala market is fed from differentiated source populations of white-bellied pangolins. Each of the 37 individuals had a unique multilocus genotype. The unbiased probability of identity (uPI) and the probability of identity among siblings (PIsibs) were both very low (uPI?=?8.443 e-21; PIsibs?=?1.011 e-07). Only five microsatellite loci were needed to reach the conservative value of PIsibs?<?0.01, overall indicating a powerful discriminating power of our combined loci. These 20 newly developed microsatellite loci might prove useful in tracing the local-to-global trade of the white-bellied pangolin, and will hopefully contribute to the DNA-assisted implementation of future conservation strategies at reasonable costs.

| S-EPMC7230135 | biostudies-literature

Isolation, characterization, and cross-amplification of 20 microsatellite markers for <i>Conospermum undulatum</i> (Proteaceae).

Project description:PremiseRecent habitat fragmentation is posing a risk to the wavy-leaved smokebush, Conospermum undulatum (Proteaceae), a rare plant species endemic to southwestern Western Australia. Microsatellite markers are required to characterize the genetic diversity and structure of the species for conservation purposes and to facilitate ecological studies.Methods and resultsIllumina MiSeq high-throughput sequencing was used to develop 20 novel microsatellite markers for C. undulatum. Polymorphism at each locus was assessed using 72 individuals from three natural populations. Nineteen markers were polymorphic, with the number of alleles per locus ranging from two to 21, and observed and expected heterozygosity ranging from 0.000 to 1.000 and 0.117 to 0.919, respectively. All markers successfully amplified in three congeneric species (C. stoechadis, C. canaliculatum and C. triplinervium).ConclusionsThe microsatellite markers will be useful for revealing patterns of genetic diversity, dispersal dynamics, and hybridization events for C. undulatum to inform future conservation efforts.

| S-EPMC6711349 | biostudies-literature

Isolation and characterization of twelve polymorphic microsatellite markers in the endangered <i>Hopea hainanensis</i> (Dipterocarpaceae).

Project description:Microsatellite markers were isolated and characterized for Hopea hainanensis Merrill & Chun, an endangered tree species with scattered distribution in Hainan Island and northern Vietnam. Twenty-six microsatellite markers were developed based on next-generation sequencing data and were genotyped by capillary electrophoresis on an ABI 3730xl DNA Analyzer. Twelve markers were found to be polymorphic in H. hainanensis. GENODIVE analyses indicated that the number of alleles ranged from 2 to 6 per locus, and the observed and expected heterozygosity varied from 0 to 0.755 and from 0.259 to 0.779, respectively. Primer transferability was tested with Hopea chinensis Hand.-Mazz. and Hopea reticulata Tardieu, in which 3 and 7 microsatellite markers were found to be polymorphic, separately. The results showed that H. reticulata and H. hainanensis had similar levels of genetic diversity. A neighbor joining dendrogram clustered all individuals into two major groups, one of which was exclusively constituted by H. hainanensis, while the other consisted of two subgroups, corresponding to H. reticulata and H. chinensis, respectively. The 12 polymorphic microsatellite markers could be applied to study genetic diversity, population differentiation, mating system, and fine-scale spatial genetic structures of H. hainanensis as well as its close relatives, facilitating the conservation and restoration of these endangered but valuable Hopea species.

| S-EPMC7790650 | biostudies-literature

Development and characterization of 20 polymorphic microsatellite markers for Epinephelus marginatus (Lowe, 1834) (Perciformes: Epinephelidae) using 454 pyrosequencing.

Project description:The dusky grouper, Epinephelus marginatus, is a well-known and widespread marine fish assessed as endangered by the International Union for the Conservation of Nature. Analyzing the genetic diversity of this species is, therefore, of utmost importance and necessary for conservation purposes. Microsatellites are molecular tools with advantages that are ideal for population analyses. This study provides the first set of species-specific microsatellite loci for E. marginatus that can be applied when assessing both intra- and interpopulation genetic variation. Twenty microsatellite loci were isolated and characterized for the dusky grouper by genotyping 20 individuals obtained from the North Eastern Atlantic Ocean (n = 4) and from the South Western Atlantic Ocean (n = 16). The number of alleles per locus varied from 2 to 11, while the observed and expected heterozygosities ranged from 0.25 to 0.94 and 0.34 to 0.89, respectively. The polymorphic information content varied from moderately to highly informative. This suite of markers provides the first specific nuclear tools for E. marginatus and, thus, allows to assess with more specificity different populations' structures.

| S-EPMC6428119 | biostudies-literature

Isolation and characterization of 13 new polymorphic microsatellite markers in the Phaseolus vulgaris L. (Common Bean) genome.

Project description:In this study, 13 polymorphic microsatellite markers were isolated from the Phaseolus vulgaris L. (common bean) by using the Fast Isolation by AFLP of Sequence COntaining Repeats (FIASCO) protocol. These markers revealed two to seven alleles, with an average of 3.64 alleles per locus. The polymorphic information content (PIC) values ranged from 0.055 to 0.721 over 13 loci, with a mean value of 0.492, and 7 loci having PIC greater than 0.5. The expected heterozygosity (H(E)) and observed heterozygosity (H(O)) levels ranged from 0.057 to 0.814 and from 0.026 to 0.531, respectively. Cross-species amplification of the 13 prime pairs was performed in its related specie of Vigna unguiculata L. Seven out of all these markers showed cross-species transferability. These markers will be useful for future genetic diversity and population genetics studies for this agricultural specie and its related species.

| S-EPMC3472738 | biostudies-literature

Isolation and characterization of nine polymorphic microsatellite markers for the deep-sea shrimp Nematocarcinus lanceopes (Crustacea: Decapoda: Caridea).

Project description:BackgroundThe shrimp Nematocarcinus lanceopes Bate, 1888 is found in the deep sea around Antarctica and sub-Antarctic islands. Previous studies on mitochondrial data and species distribution models provided evidence for a homogenous circum-Antarctic population of N. lanceopes. However, to analyze the fine-scale population genetic structure and to examine influences of abiotic environmental conditions on population composition and genetic diversity, a set of fast evolving nuclear microsatellite markers is required.FindingsWe report the isolation and characterization of nine polymorphic microsatellite markers from the Antarctic deep-sea shrimp species Nematocarcinus lanceopes (Crustacea: Decapoda: Caridea). Microsatellite markers were screened in 55 individuals from different locations around the Antarctic continent. All markers were polymorphic with 9 to 25 alleles per locus. The observed heterozygosity ranged from 0.545 to 0.927 and the expected heterozygosity from 0.549 to 0.934.ConclusionsThe reported markers provide a novel tool to study genetic structure and diversity in Nematocarcinus lanceopes populations in the Southern Ocean and monitor effects of ongoing climate change in the region on the populations inhabiting these.

| S-EPMC3629709 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data