Browse
Submit Data
Databases
API
Help

Dataset Information

30 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Characterization of 13 microsatellite markers for Diuris basaltica (Orchidaceae) and related species.

ABSTRACT: UNLABELLED: PREMISE OF THE STUDY:Diuris basaltica (Orchidaceae) is an endangered forb on the Victorian grasslands and has many close relatives. Microsatellite markers have been developed to facilitate assessment of population structure within D. basaltica and among related taxa within the species complex. • METHODS AND RESULTS:Twenty-five microsatellite markers (13 polymorphic and 12 monomorphic) were developed from D. basaltica using 454 pyrosequencing, and all primer pairs were amplified in D. gregaria and D. chryseopsis. For the set of polymorphic markers, the number of alleles per locus ranged from one to 10, two to nine, and two to 18 for D. basaltica, D. gregaria, and D. chryseopsis, respectively. The expected and observed heterozygosities ranged from 0.18 to 0.95 and 0.14 to 0.86, respectively. • CONCLUSIONS:The microsatellite markers developed in this study can be used to analyze the population genetic structure of D. basaltica and other Diuris species.

SUBMITTER: Ahrens CW

PROVIDER: S-EPMC4104714 | biostudies-literature | 2014 Jan

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Characterization of 13 microsatellite markers for Diuris basaltica (Orchidaceae) and related species.

Ahrens Collin W CW James Elizabeth A EA

Applications in plant sciences 20140107 1

<h4>Unlabelled</h4><h4>Premise of the study</h4>Diuris basaltica (Orchidaceae) is an endangered forb on the Victorian grasslands and has many close relatives. Microsatellite markers have been developed to facilitate assessment of population structure within D. basaltica and among related taxa within the species complex. •<h4>Methods and results</h4>Twenty-five microsatellite markers (13 polymorphic and 12 monomorphic) were developed from D. basaltica using 454 pyrosequencing, and all primer pair ...[more]

PMID: 25202591

Similar Datasets

Microsatellite markers for Corybas (Orchidaceae) species in New Zealand.

Project description:Premise of the Study:Microsatellite markers were developed for New Zealand species of Corybas (Orchidaceae) to investigate population genetics and species delimitation. Methods and Results:From sequencing a total genomic DNA library (using Illumina MiSeq), we developed 22 microsatellite markers for C. obscurus. The di- and trinucleotide repeat loci were initially trialed on individuals representing seven Corybas taxa (C. "rimutaka," C. confusus, C. hypogaeus, C. macranthus, C. obscurus, C. trilobus, and C. walliae) and had one to eight alleles per locus. Twelve polymorphic markers were further tested on six Corybas populations from three of the seven taxa (C. obscurus, C. "rimutaka," and C. trilobus). Observed and expected heterozygosities ranged from 0-1 and 0-0.859, respectively. The utility of these 12 loci was further validated in five related Corybas species (C. hypogaeus, C. obscurus, C. vitreus, C. walliae, and C. "rimutaka"; 38 individuals) representing populations from across the North and South Islands. The average value for genetic diversity among populations (F ST) of 0.439 shows differentiation among species. Conclusions:These markers will be useful for future studies aimed at delimiting species boundaries and examining the genetic diversity of the New Zealand Corybas species.

| S-EPMC6240450 | biostudies-literature

Development of microsatellite markers for <i>Cypripedium tibeticum</i> (Orchidaceae) and their applicability to two related species.

Project description:Premise of the studyTo investigate genetic diversity and structure, microsatellite markers were developed and characterized for Cypripedium tibeticum, an endangered orchid species, and their utility tested in two relatives: C. flavum and C. bardolphianum.Methods and resultsCandidate microsatellite loci were isolated based on next-generation sequencing. We identified 20 polymorphic loci with di- or trinucleotide repeats in three populations of C. tibeticum. Genotyping results showed the total number of alleles per locus varied from two to 21, and the observed and expected heterozygosity ranged from 0.261 to 0.967 and 0.441 to 0.960, respectively. Cross-species amplification showed most of the markers were applicable to C. flavum and C. bardolphianum.ConclusionsThe 20 polymorphic microsatellite markers developed in this study are useful tools for studying the conservation genetics and phylogeography of C. tibeticum and its related species.

| S-EPMC5749819 | biostudies-literature

Characterization of microsatellite markers for <i>Moricandia moricandioides</i> (Brassicaceae) and related species.

Project description:Premise of the studyPolymorphic microsatellite markers were developed to study population structure and mating patterns of the monocarpic herb Moricandia moricandioides (Brassicaceae).Methods and resultsIllumina MiSeq sequencing was used to develop a panel of 15 polymorphic microsatellite markers that were tested across 77 individuals from three populations on the Iberian Peninsula. All markers were polymorphic in at least two studied populations, and the number of alleles ranged from one to 11 per locus. The levels of observed and expected heterozygosity ranged from 0.000 to 1.000 and from 0.153 to 0.865, respectively. Nine and 11 loci were successfully amplified in the congeneric species M. arvensis and M. foetida, respectively.ConclusionsThe 15 microsatellite markers will be useful for population genetic studies of the genus Moricandia. These markers will serve as a useful tool for exploring population structure and mating patterns of M. moricandioides.

| S-EPMC6110244 | biostudies-literature

Characterization of 15 nuclear microsatellite markers for <i>Afzelia africana</i> (Fabaceae) and related species.

Project description:PremiseAfzelia africana (Fabaceae) is a valuable, internationally vulnerable tree species in tropical Africa. The development of specific simple sequence repeat (SSR) loci is necessary for population genetic studies in this tree species and its closest relatives.Methods and resultsFifteen new polymorphic microsatellite markers were developed for A. africana using Illumina next-generation sequencing. We tested the polymorphism of the 15 loci in three populations in Benin, West Africa. The number of expressed alleles per locus varied from one to 12. The levels of observed and expected heterozygosity ranged from 0.100 to 1.000 and from 0.095 to 0.882, respectively. Most markers successfully amplified in the closely related species A. quanzensis and A. bipindensis, but less so in A. bipindensis.ConclusionsBecause of their cross-amplification ability, these newly developed loci will serve as useful tools for future molecular analyses on A. africana and related species.

| S-EPMC6526647 | biostudies-literature

Characterization of microsatellite markers for the endangered <i>Daphne rodriguezii</i> (Thymelaeaceae) and related species.

Project description:PremiseThe endangered shrub Daphne rodriguezii (Thymelaeaceae) is endemic to the Balearic island of Menorca, where fragmentation and severe population decline are ongoing threats to this taxon. We developed a set of microsatellite markers to analyze the fine-scale genetics of its few extant populations.Methods and resultsFifteen microsatellite markers were obtained through Illumina high-throughput sequencing and tested in two populations. Twelve of these loci showed no evidence of null alleles and were highly polymorphic, with a mean number of 8.3 alleles per locus. Levels of observed and expected heterozygosity ranged from 0.100 to 0.952 and from 0.095 to 0.854, respectively. Seven to nine of these loci were successfully amplified in five other Daphne species.ConclusionsThis set of markers provides a useful tool for investigating the factors driving fine-scale population structure in this threatened species, and it represents a novel genetic resource for other European Daphne species.

| S-EPMC6636617 | biostudies-literature

Characterization of 13 microsatellite markers for Calochortus gunnisonii (Liliaceae) from Illumina MiSeq sequencing.

Project description:Microsatellite primers were designed for Calochortus gunnisonii (Liliaceae), a montane lily species of the central and southern Rocky Mountains, using next-generation DNA sequencing. The markers will be used to investigate population structure, genetic diversity, and demographic history. Thirteen polymorphic microsatellite loci were isolated from C. gunnisonii using Illumina MiSeq next-generation DNA sequencing and bioinformatic screening. The mean number of alleles per locus ranged from 4.15 to 5.92 (avg. = 4.97). Observed and expected heterozygosity ranged from 0.077 to 0.871 and 0.213 to 0.782, respectively. The primers were also tested for cross-species amplification value with C. flexuosus, C. nuttallii, C. kennedyi var. kennedyi, and C. subalpinus. These primers will be useful for genetic and evolutionary studies across C. gunnisonii's range within the southern and central Rocky Mountains. Furthermore, these markers have proven valuable for cross-species amplifications within Calochortus.

| S-EPMC4542947 | biostudies-literature

Development and characterization of nuclear microsatellite markers for Eremanthus erythropappus and their transferability across related species.

Project description:BACKGROUND:We developed simple sequence repeats (SSR) for Eremanthus erythropappus (DC.) MacLeish, an endangered tree species endemic to the Brazilian Savanna and Atlantic Forest biomes, and tested their transferability to two closely related Eremanthus species. RESULTS:Using a genomic library enriched with tandem repeat motifs, we identified 16 primer pairs, and characterized them in two populations. Nine primers amplified the expected size fragments and seven SSRs were polymorphic, providing a total of 38 alleles and an average of 4.22 alleles per marker. The polymorphic information content (PIC) ranged from 0.44 to 0.94 with an average of 0.65. The average observed heterozygosity across all loci varied from 0.61 to 1.00. The observed (HO) and expected (HE) heterozygosity within the two populations varied from 0.65 to 1.00 and from 0.31 to 1.00, respectively. CONCLUSIONS:These newly developed SSR markers are a powerful tool for population genetic analyses and may be useful in studies on species ecology, evolution, and taxonomy.

| S-EPMC7341598 | biostudies-literature

Development and characterization of microsatellite markers for the medicinal plant Smilax brasiliensis (Smilacaceae) and related species.

Project description:A new set of microsatellite or simple sequence repeat (SSR) markers were developed for Smilax brasiliensis, which is popularly known as sarsaparilla and used in folk medicine as a tonic, antirheumatic, and antisyphilitic. Smilax brasiliensis is sold in Brazilian pharmacies, and its origin and effectiveness are not subject to quality control. • Using a protocol for genomic library enrichment, primer pairs were developed for 26 microsatellite loci and validated in 17 accessions of S. brasiliensis. Thirteen loci were polymorphic and four were monomorphic. The primers successfully amplified alleles in the congeners S. campestris, S. cissoides, S. fluminensis, S. goyazana, S. polyantha, S. quinquenervia, S. rufescens, S. subsessiliflora, and S. syphilitica. • The new SSR markers described herein are informative tools for genetic diversity and gene flow studies in S. brasiliensis and several congeners.

| S-EPMC4105028 | biostudies-literature

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

Transferability and characterization of microsatellite markers in two Neotropical Ficus species.

Project description:Microsatellite markers were transferred and characterized for two Neotropical fig tree species, Ficus citrifolia and Ficus eximia. Our study demonstrated that microsatellite markers developed from different subgenera of Ficus can be transferred to related species. In the present case, 12 of the 15 primer pairs tested (80%) were successfully transferred to both of the above species. Eleven loci were polymorphic when tested across 60 F. citrifolia and 60 F. eximia individuals. For F. citrifolia, there were 4 to 15 alleles per locus, whereas expected heterozygosities ranged from 0.31 to 0.91. In the case of F. eximia, this was 2 to 12 alleles per locus and expected heterozygosities from 0.42 to 0.87.

| S-EPMC3036046 | 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