Browse
Submit Data
Databases
API
Help

Dataset Information

32 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Development of 18 microsatellite markers for Salvia pratensis.

ABSTRACT: Premise:Microsatellite markers were developed for the perennial herb Salvia pratensis (Lamiaceae), a species representative of European dry grasslands. The development of microsatellite markers is needed for genetic and phylogeographical studies of species from the genus Salvia. Methods and Results:We used low-coverage Illumina sequencing to identify microsatellite loci. Based on these data, we have developed 18 polymorphic microsatellite markers with the number of alleles per locus ranging from two to 15. The levels of observed and expected heterozygosity ranged from 0.05 to 0.95 and from 0.05 to 0.89, respectively. The majority of the markers successfully cross-amplified in other Salvia species. Conclusions:The markers were shown to be suitable for population genetic and phylogeographic studies in S. pratensis as well as in related species (S. aethiopis, S. austriaca, S. glutinosa, S. nemorosa, S. nutans, and S. verticillata) and will be used in the broader context to trace the origins of European dry grasslands.

SUBMITTER: Krak K

PROVIDER: S-EPMC6976894 | biostudies-literature | 2020 Jan

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Development of 18 microsatellite markers for <i>Salvia pratensis</i>.

Krak Karol K Vít Petr P Douda Jan J Mandák Bohumil B

Applications in plant sciences 20200122 1

<h4>Premise</h4>Microsatellite markers were developed for the perennial herb <i>Salvia pratensis</i> (Lamiaceae), a species representative of European dry grasslands. The development of microsatellite markers is needed for genetic and phylogeographical studies of species from the genus <i>Salvia</i>.<h4>Methods and results</h4>We used low-coverage Illumina sequencing to identify microsatellite loci. Based on these data, we have developed 18 polymorphic microsatellite markers with the number of a ...[more]

PMID: 31993258

Similar Datasets

Development of 18 microsatellite markers for <i>Atractylodes japonica</i>.

Project description:PremiseAtractylodes japonica (Asteraceae) is endemic to East Asia, where its rhizomes are used in traditional medicine. To investigate the genetic diversity of this species, we developed polymorphic microsatellite markers.Methods and resultsWe obtained a total of 175,825 simple sequence repeat (SSR) loci using the Illumina HiSeq 2500 system. Eighteen polymorphic SSR primer pairs were selected to determine heterozygosity levels and allele numbers in 80 individuals from four A. japonica populations. The levels of observed and expected heterozygosity ranged from 0.000 to 1.000 and from 0.133 to 0.892, respectively. Cross-amplification in the related species A. macrocephala and A. lancea was successful in 15 and 14 of the 18 markers, respectively.ConclusionsThese microsatellite markers will be useful for future studies involving A. japonica population genetics and breeding.

| S-EPMC7249270 | biostudies-literature

Development of 18 polymorphic microsatellite markers for Vinca minor (Apocynaceae) via 454 pyrosequencing.

Project description:Polymorphic microsatellite markers were developed in Vinca minor (Apocynaceae) to evaluate the level of clonality, population structure, and genetic diversity of the species within its native and introduced range. A total of 1371 microsatellites were found in 43,565 reads from 454 pyrosequencing of genomic V. minor DNA. Additional microsatellite loci were mined from publicly available cDNA sequences. After several rounds of screening, 18 primer pairs flanking di-, tri-, or tetranucleotide repeats were identified that revealed high levels of genetic diversity in two native Italian populations, with two to 11 alleles per locus. Clonal growth predominated in two populations from the introduced range in Germany. Five loci successfully cross-amplified in three additional Vinca species. The novel polymorphic microsatellite markers are promising tools for studying clonality and population genetics of V. minor and for assessing the historical origin of Central European populations.

| S-EPMC4435468 | biostudies-literature

Salvia pratensis

Project description:Salvia pratensis Raw sequence reads

| PRJNA564705 | ENA

Development of new microsatellite markers for Salvia officinalis L. and its potential use in conservation-genetic studies of narrow endemic Salvia brachyodon Vandas.

Project description:Nine new microsatellite markers (SSR) were isolated from Salvia officinalis L. A total of 125 alleles, with 8 to 21 alleles per locus, were detected in a natural population from the east Adriatic coast. The observed heterozygosity, expected heterozygosity, and polymorphic information content ranged from 0.46 to 0.83, 0.73 to 0.93 and 0.70 to 0.92, respectively. New microsatellite markers, as well as previously published markers, were tested for cross-amplification in Salvia brachyodon Vandas, a narrow endemic species known to be present in only two localities on the Balkan Peninsula. Out of 30 microsatellite markers tested on the natural S. brachyodon population, 15 were successfully amplified. To obtain evidence of recent bottleneck events in the populations of both species, observed genetic diversity (H(E)) was compared to the expected genetic diversity at mutation-drift equilibrium (H(EQ)) and calculated from the observed number of alleles using a two-phased mutation model (TPM). Recent bottleneck events were detected only in the S. brachyodon population. This result suggests the need to reconsider the current threat category of this endemic species.

| S-EPMC3472793 | biostudies-literature

Development of microsatellite markers for Eurya acuminatissima (Theaceae).

Project description:PREMISE OF THE STUDY:Sixteen microsatellite markers were developed to study the fine-scale spatial genetic structure of Eurya acuminatissima, a dioecious tree species of Theaceae endemic to southern China. METHODS AND RESULTS:A total of 30 primer pairs were initially designed and tested on the basis of the transcriptome data of E. acuminatissima, of which 16 were successfully amplified and showed clear polymorphism. For these microsatellites, one to 17 alleles per locus were identified. The observed and expected heterozygosities ranged from 0 to 1.000 and 0 to 0.903, respectively. CONCLUSIONS:The microsatellite markers described here can be used to study genetic diversity and spatial genetic structure of E. acuminatissima. Furthermore, all loci were successfully cross-amplified in a related species, E. auriformis.

| S-EPMC5546169 | biostudies-literature

Development of microsatellite markers for Carallia brachiata (Rhizophoraceae).

Project description:Microsatellite markers were developed for Carallia brachiata to assess the genetic diversity and structure of this terrestrial species of the Rhizophoraceae. Based on transcriptome data for C. brachiata, 40 primer pairs were initially designed and tested, of which 18 were successfully amplified and 11 were polymorphic. For these microsatellites, one to three alleles per locus were identified. The observed and expected heterozygosities ranged from 0 to 0.727 and 0 to 0.520, respectively. In addition, all primers were successfully amplified in two congeners: C. pectinifolia and C. garciniifolia. The microsatellite markers described here will be useful in population genetic studies of C. brachiata and related species, suggesting that developing microsatellite markers from next-generation sequencing data can be efficient for genetic studies across this genus.

| S-EPMC4356322 | biostudies-literature

Development of microsatellite markers for Isodon longitubus (Lamiaceae).

Project description:Microsatellite markers were developed for Isodon longitubus to study the natural hybridization of the species and its congeners. • A total of 10 primer sets were developed for I. longitubus. From the initial screening, all of 10 loci were polymorphic with five to 19 alleles per locus in the Mt. Ishizuchi population, whereas nine loci were polymorphic with two to 12 alleles per loci in the Toon population. Although one locus was monomorphic at one population, the observed and expected heterozygosity values estimated from 34 I. longitubus samples ranged from 0.273 to 1.000 and from 0.483 to 0.918, respectively. Six primer sets could amplify all three species examined in this study (I. inflexus, I. japonicus, and I. shikokianus). • The 10 microsatellite markers developed here will be useful in analyzing the population genetic structure of I. longitubus and in studying the natural hybridization between Isodon species.

| S-EPMC4103467 | biostudies-literature

Development of microsatellite markers for Crepis mollis (Asteraceae).

Project description:Polymorphic microsatellite markers were developed for the threatened species Crepis mollis (Asteraceae) to investigate population and conservation genetics. Illumina sequencing was conducted on pooled genomic DNA from 10 individuals of two populations. Ten polymorphic and 10 monomorphic microsatellite loci with di-, tri-, tetra-, penta-, and hexanucleotide repeat motifs were developed and characterized in C. mollis. In the polymorphic markers, up to 17 alleles per locus were detected with an observed and expected heterozygosity ranging from 0.120 to 0.780 and 0.102 to 0.834, respectively. Furthermore, the polymorphic markers were tested for cross-amplification in three congeneric species (C. biennis, C. foetida, and C. sancta) and amplified in up to three loci. The markers developed in this study are the first microsatellites tested on C. mollis and will be useful for performing population and conservation genetic studies in this threatened species.

| S-EPMC4948905 | biostudies-literature

Isolation and characterization of chromosomal markers in Poa pratensis.

Project description:BACKGROUND:Poa pratensis L. is a turf grass and forage crop used worldwide. Being a facultative apomictic species, P. pratensis has a highly variable chromosome number. Chromosomal markers constitute a powerful tool for chromosome identification and for various aspects of genomic research. However, currently, no chromosomal markers are available for P. pratensis. RESULTS:Four novel chromosome markers were isolated from a screen of Cot-1 DNA libraries, combined with fluorescence in situ hybridization (FISH) in Poa pratensis. Three tandemly repetitive sequences (PpTR-1, PpTR-2, and PpTR-3) were characterized as subtelomeric. Monomers of 318 bp, 189 bp and 189 bp were identified in PpTR-1, PpTR-2, and PpTR-3, respectively. One tandemly repetitive sequence (PpCR-1) was shown to be centromeric or pericentromeric, and it had a monomer of 27 bp. The distribution patterns of PpTR-1, PpTR-2, and PpTR-3 were highly conserved across different P. pratensis cultivars and in the distantly related Poa species, whereas PpCR-1 was conserved across different P. pratensis cultivars, but less conserved across Poa species. CONCLUSION:In this study, we report the identification and characterization of four novel chromosomal markers in P. pratensis. These chromosomal markers are powerful tools for accurate assessment of chromosome count, genomic and phylogenetic analyses, as well as studies of apomixis in P. pratensis.

| S-EPMC5345224 | 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

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