Browse
Submit Data
Databases
API
Help

Dataset Information

25 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Development, characterization, and cross-amplification of 17 microsatellite markers for Filipendula vulgaris.

ABSTRACT: Premise:Polymorphic microsatellite markers were developed as a tool for genetic investigations of Filipendula vulgaris (Rosaceae) and related species. Methods and Results:Seventeen new polymorphic microsatellite markers were developed for F. vulgaris using the Illumina MiSeq platform. Polymorphism of the 17 loci was tested in three populations. We identified a total of 203 alleles, ranging from four to 19 per locus, with levels of observed and expected heterozygosity ranging from 0.267 to 1.000 and 0.461 to 0.899, respectively. Primers were also tested for cross-amplification in three related species. Seven loci successfully cross-amplified in F. camtschatica and F. ulmaria, whereas we detected positive cross-amplification in only three loci in Geum urbanum. Conclusions:The newly developed microsatellite primers will serve as useful genetic tools for further population genetic studies on F. vulgaris and related species.

SUBMITTER: Cortan D

PROVIDER: S-EPMC6923706 | biostudies-literature | 2019 Dec

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Development, characterization, and cross-amplification of 17 microsatellite markers for <i>Filipendula vulgaris</i>.

Čortan Dijana D Krak Karol K Vít Petr P Mandák Bohumil B

Applications in plant sciences 20191208 12

<h4>Premise</h4>Polymorphic microsatellite markers were developed as a tool for genetic investigations of <i>Filipendula vulgaris</i> (Rosaceae) and related species.<h4>Methods and results</h4>Seventeen new polymorphic microsatellite markers were developed for <i>F. vulgaris</i> using the Illumina MiSeq platform. Polymorphism of the 17 loci was tested in three populations. We identified a total of 203 alleles, ranging from four to 19 per locus, with levels of observed and expected heterozygosity ...[more]

PMID: 31890353

Similar Datasets

Microsatellite markers for Anthericum ramosum: Development, characterization, and cross-species amplification.

Project description:Premise:A set of polymorphic nuclear microsatellite loci was developed and tested for use in population genetic analyses of Anthericum ramosum (Agavaceae) and related species. Methods and Results:Sequences of 110 primers were extracted in silico from Illumina MiSeq genome skimming data. The degree of polymorphism of 19 loci was tested in four A. ramosum populations collected in Central and Eastern Europe. The average number of alleles per loci ranged from two to 17, and levels of observed and expected heterozygosity ranged from 0.000 to 1.000 and from 0.100 to 0.900, respectively. Primers were successfully amplified in the closely related species A. liliago (12 loci) and Chlorophytum comosum (six loci), whereas they mostly failed to amplify in the phylogenetically more-distant species Muscari comosum (three loci) and M. tenuiflorum (no amplification). Conclusions:This newly developed set of polymorphic nuclear microsatellite markers will be useful for population genetic investigation of A. ramosum and closely related species.

| S-EPMC7035427 | biostudies-literature

Development, characterization, and cross-amplification of microsatellite markers for <i>Psammosilene tunicoides</i> (Caryophyllaceae).

Project description:Premise of the studyPsammosilene tunicoides (Caryophyllaceae) is a narrowly distributed and endemic plant species in southwestern China. The overexploitation of natural P. tunicoides has led to the destruction of many populations. Population and genetic studies will provide crucial data for the protection and management of P. tunicoides. In this study, we develop simple sequence repeat markers of P. tunicoides to analyze population diversity.Methods and resultsMicrosatellite loci of P. tunicoides were isolated with FIASCO. Eleven polymorphic and 10 monomorphic primers were developed. The 11 polymorphic primers were tested in three P. tunicoides populations, yielding two to nine alleles per locus. Levels of observed heterozygosity varied from 0.000 to 1.000, and levels of expected heterozygosity ranged from 0.000 to 0.615. In addition, three of these loci were successfully amplified, and showed polymorphism, in three Silene species.ConclusionsThese microsatellite markers can be valuable tools to investigate the genetic diversity and population structure of P. tunicoides.

| S-EPMC6303153 | biostudies-literature

Development and characterization of 17 microsatellite markers for Sonchus oleraceus.

Project description:Premise:The common sowthistle, Sonchus oleraceus (Asteraceae), is a globally invasive weedy species. In order to investigate its genetic diversity, population genetic structure, and evolutionary history, we developed and characterized nuclear simple sequence repeat markers (SSRs or microsatellites). Methods and Results:Seventeen microsatellite primer pairs were developed based on the Illumina sequence data. Ten developed SSR loci were polymorphic in four populations sampled from broad geographical regions. The number of alleles per locus ranged from one to 11, and the levels of observed and expected heterozygosity ranged from 0.000 to 1.000 and from 0.000 to 0.801, respectively. Up to 82% of the newly developed primer pairs were successfully amplified in the congeneric taxa S. asper, S. asper subsp. glaucescens, S. canariensis, and S. palmensis. Conclusions:The SSR markers developed in this study will be useful for future population genetic studies on S. oleraceus and other congeneric species.

| S-EPMC7073324 | biostudies-literature

Development, characterization, and cross-amplification of microsatellite markers in the understudied African genus Anthonotha (Fabaceae).

Project description:PREMISE OF THE STUDY:Anthonotha macrophylla (Fabaceae) is a common tree species throughout the Guineo-Congolian forest that is sometimes confounded with other congeneric species; it is expected to be an interesting phylogeographical model to infer the history of the African dense forests. We developed 18 microsatellite markers from this species and tested their transferability in 15 congeneric species. METHODS AND RESULTS:A genomic library was obtained using the Illumina platform, and 18 polymorphic microsatellite loci were developed. The polymorphic microsatellites displayed two to 24 alleles (average: 11.9 alleles per locus, expected heterozygosity range: 0.18-0.91, mean: 0.64) in three populations of A. macrophylla from Benin, Liberia, and Cameroon. Cross-amplification in one to nine individuals of 15 congeneric Anthonotha species (A. acuminata, A. brieyi, A. cladantha, A. crassifolia, A. ferruginea, A. fragrans, A. gilletii, A. lamprophylla, A. mouandzae, A. noldeae, A. pellegrinii, A. pynaertii, A. stipulacea, A. wijmacampensis, and A. xanderi) showed successful amplification in six to 17 loci, making most of these markers useful at the generic level. CONCLUSIONS:This set of markers will be useful to study species delimitation and the genetic structure of Anthonotha species, and thus to better understand the history of tropical African rainforests.

| S-EPMC5231917 | biostudies-literature

Development of 12 chloroplast microsatellite markers in Vigna unguiculata (Fabaceae) and amplification in Phaseolus vulgaris.

Project description:UnlabelledPremise of the studyVigna unguiculata is an economically important legume, and the complexity of its variability and evolution needs to be further understood. Based on publicly available databases, we developed chloroplast microsatellite primers to investigate genetic diversity within V. unguiculata and its related species Phaseolus vulgaris. •Methods and resultsTwelve polymorphic chloroplast microsatellite markers were developed and characterized in 62 V. unguiculata individuals. The number of alleles per locus varied between two and four, the unbiased haploid diversity per locus ranged from 0.123 to 0.497, and the polymorphism information content varied from 0.114 to 0.369. In cross-species amplifications, nine of these markers showed polymorphism in 29 P. vulgaris individuals. •ConclusionsThe newly developed chloroplast microsatellite markers exhibit variation in V. unguiculata as well as their transferability in P. vulgaris. These markers can be used to investigate genetic diversity and evolution in V. unguiculata and P. vulgaris.

| S-EPMC4103102 | biostudies-literature

Development, characterization, and cross-amplification of polymorphic microsatellite markers for North American Trachymyrmex and Mycetomoellerius ants.

Project description:ObjectiveThe objective of this study is to develop and identify polymorphic microsatellite markers for fungus-gardening (attine) ants in the genus Trachymyrmex sensu lato. These ants are important ecosystem engineers and have been a model group for understanding complex symbiotic systems, but very little is understood about the intraspecific genetic patterns across most North American attine species. These microsatellite markers will help to better study intraspecific population genetic structure, gene flow, mating habits, and phylogeographic patterns in these species and potentially other congeners.ResultsUsing next-generation sequencing techniques, we identified 17 and 12 polymorphic microsatellite markers from T. septentrionalis and Mycetomoellerius (formerly Trachymyrmex) turrifex, respectively, and assessed the genetic diversity of each marker. We also analyzed the cross-amplification success of the T. septentrionalis markers in two other closely related Trachymyrmex species, and identified 10 and 12 polymorphic markers for T. arizonensis and T. pomonae, respectively.

| S-EPMC7092486 | biostudies-literature

Development and characterization of 16 novel microsatellite markers by Transcriptome sequencing for Angelica dahurica and test for cross-species amplification.

Project description:BackgroundAngelica dahurica (Apiaceae) is an important herb in traditional Chinese medicine. Because of its important medicinal and economic values, its wild resources were over-exploited and increasingly reduced. Meanwhile, the diversity of cultivars of A. dahurica has decreased as a result of long-term artificial cultivation. However, there are no population genetics studies of natural A. dahurica reported yet, especially for using microsatellite markers (SSRs) to investigate population genetics of the species.ResultsSixteen polymorphic EST-SSR loci were isolated from A. dahurica with transcriptome sequencing technology (RNA-Seq). The number of alleles varied from 2 to 15 per polymorphic locus over populations with the observed and expected heterozygosities ranging from 0.000 to 1.000 and from 0.000 to 0.829, respectively. Significant deviations from Hardy-Weinberg equilibrium were observed at 8 loci. Tests of linkage disequilibrium showed 11 informative locus pairs were significant across all populations. Cross-species amplification showed that 14 out of 16 SSR loci have the transferability in cultivar-A. dahurica cv. 'Hangbaizhi' and A. decursiva.ConclusionsThe 16 newly developed loci microsatellite primers with RNA-Seq will be useful for further investigating population genetics of A. dahurica, cultivars and other members of this genus.

| S-EPMC7140362 | 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

Development, characterization, and cross-amplification of 16 microsatellite primers for Atriplex tatarica (Amaranthaceae).

Project description:Premise of the study:Microsatellite primers were developed to characterize the genetic diversity and structure of the annual herb Atriplex tatarica (Amaranthaceae) and to facilitate ecological and evolutionary studies of A. tatarica and its relatives. Methods and Results:Sixteen novel microsatellite primers were developed for A. tatarica based on high-throughput sequencing of enriched libraries. All markers were polymorphic, with the number of alleles per locus ranging from three to 25 and observed and expected heterozygosity ranging from 0.08 to 0.74 and 0.10 to 0.87, respectively. In addition, some of these loci were successfully amplified and showed polymorphisms in four Atriplex and seven Chenopodium species. Conclusions:The microsatellite markers published here will be useful in assessing genetic diversity, structure, and gene flow within and across populations of A. tatarica, as well as in other species of Atriplex and the related genus Chenopodium.

| S-EPMC5703183 | biostudies-literature

Development of 15 microsatellite markers in Acer triflorum (Aceraceae) and cross-amplification in congeneric species.

Project description:Premise of the Study:Acer (Aceraceae) is an important genus in forest ecosystems in the Northern Hemisphere. In China, 151 species have been reported, and approximately 61 species are endemic. Thus, China is considered to host the greatest diversity of Acer, but markers are needed to evaluate the genetic structure and genetic diversity of these populations of wild Acer species. Methods and Results:Using an enriched genomic library, we developed and characterized 15 microsatellite primers for A. triflorum, 10 of which were polymorphic. The number of alleles varied from one to nine. The levels of observed heterozygosity and expected heterozygosity per locus ranged from 0.000 to 1.000 and 0.000 to 0.826, respectively. Most primers also successfully amplified in A. ginnala, A. griseum, A. mandshuricum, A. pseudosieboldianum, A. sinopurpurascens, A. tegmentosum, and A. ukurunduense. Conclusions:These markers from A. triflorum will provide an opportunity to study genetic diversity and genetic structure in the genus Acer.

| S-EPMC6055552 | 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