Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Development and characterization of microsatellite loci in the Centricnemus leucogrammus weevil.

ABSTRACT: Centricnemus leucogrammus is a weevil characteristic of European xerothermic habitats and steppes. The species was probably more widespread during the Pleistocene glaciations, while its current distribution is limited to "warm-stage refugia." It may be regarded as a typical representative of flightless xerothermophilous beetles. Previous studies concentrated on its genetic variation using mitochondrial genes. Here, we identified, tested and characterized 24 polymorphic microsatellite loci with the use of 454 sequencing of microsatellite enriched genomic libraries. The new set of loci will be used in studies on the population structure of this weevil and may provide valuable information for its conservation.

SUBMITTER: Kajtoch L

PROVIDER: S-EPMC3486996 | biostudies-literature | 2012 Dec

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Development and characterization of microsatellite loci in the Centricnemus leucogrammus weevil.

Kajtoch Lukasz L Nadachowska-Brzyska Krystyna K Babik Wiesław W

Molecular biology reports 20121013 12

Centricnemus leucogrammus is a weevil characteristic of European xerothermic habitats and steppes. The species was probably more widespread during the Pleistocene glaciations, while its current distribution is limited to "warm-stage refugia." It may be regarded as a typical representative of flightless xerothermophilous beetles. Previous studies concentrated on its genetic variation using mitochondrial genes. Here, we identified, tested and characterized 24 polymorphic microsatellite loci with t ...[more]

PMID: 23065209

Similar Datasets

Development and characterization of microsatellite loci for Ficus hirta (Moraceae).

Project description:Microsatellite primers were developed to investigate population genetic structure in Ficus hirta (Moraceae). Sixteen microsatellite primers were developed and optimized for F. hirta using Illumina paired-end sequencing of pre-receptive and receptive developmental-phase female flowers. Out of 16 primers, nine were found to be polymorphic in four populations of F. hirta. Alleles per locus ranged from two to 15 across the 94 F. hirta individuals, while within-population observed and expected heterozygosity per locus ranged from 0.000 to 0.955 and from 0.000 to 0.882, respectively. In addition, the 16 primers were tested in 29 additional Ficus species, with all found to amplify in at least 11 of these species and with most amplifying in a majority of the species. This set of microsatellite primers is the first specifically developed for F. hirta and will facilitate studies of genetic diversity within and genetic differentiation among populations of Ficus species.

| S-EPMC4504727 | biostudies-literature

Development and characterization of microsatellite loci for Lindera glauca (Lauraceae).

Project description:Microsatellite primers were developed to investigate population genetic structure in Lindera glauca (Lauraceae). Twenty-five microsatellite primers were developed and optimized for L. glauca using Illumina's Solexa sequencing technology. These novel primers were found to be polymorphic in nine wild L. glauca populations with 81 total alleles confirmed and genotyped via capillary gel electrophoresis. The total number of alleles, observed heterozygosity, and expected heterozygosity for each population ranged from one to four, from 0.00 to 0.90, and from 0.00 to 0.79, respectively. In addition, the 25 primers were tested in 10 additional individuals of the related species L. communis, and all but four markers showed good amplification results. This set of microsatellite primers is the first specifically developed for L. glauca and will facilitate studies of genetic diversity and evolution among populations of this species.

| S-EPMC5104530 | biostudies-literature

Development and characterization of 32 microsatellite loci in Genipa americana (Rubiaceae).

Project description:Microsatellite primers were developed for the tree species Genipa americana (Rubiaceae) for further population genetic studies. • We identified 144 clones containing 65 repeat motifs from a genomic library enriched for (CT)8 and (GT)8 motifs. Primer pairs were developed for 32 microsatellite loci and validated in 40 individuals of two natural G. americana populations. Seventeen loci were polymorphic, revealing from three to seven alleles per locus. The observed and expected heterozygosities ranged from 0.24 to 1.00 and from 0.22 to 0.78, respectively. • The 17 primers identified as polymorphic loci are suitable to study the genetic diversity and structure, mating system, and gene flow in G. americana.

| S-EPMC4103104 | biostudies-literature

Development and characterization of polymorphic microsatellite loci for Saxifraga egregia (Saxifragaceae).

Project description:Saxifraga egregia (Saxifragaceae) is a perennial herb that is endemic to the Qinghai-Tibet Plateau. We developed 12 polymorphic microsatellite loci for S. egregia to investigate its population genetics. Forty-eight pairs of microsatellite primers (including 36 monomorphic loci) were isolated and characterized by magnetic bead enrichment. Twelve of these markers showed polymorphism, and the number of alleles per locus ranged from four to 14 across 50 individuals from three populations of S. egregia. No linkage disequilibrium was detected in any pair of loci. These polymorphic markers are expected to be helpful in further studies on the systematics and phylogeography of S. egregia in the Qinghai-Tibet Plateau.

| S-EPMC4542942 | biostudies-literature

Development and characterization of polymorphic microsatellite loci in Phellodendron amurense (Rutaceae).

Project description:Microsatellite markers were developed for the rare species Phellodendron amurense to assess the genetic diversity and population structure of this plant. • In total, 27 microsatellite markers were developed for P. amurense by using an enriched genomic library and hybridization; all of these primers successfully amplified DNA fragments in P. amurense. These markers were screened in 74 individuals from four populations in China; 15 loci were found to be polymorphic, with the number of alleles per locus ranging from one to nine. • The microsatellite markers developed here represent a useful tool for studying the population genetic structure of P. amurense and to inform toward the development of effective conservation programs for this species.

| S-EPMC4105284 | biostudies-literature

Development and characterization of 23 microsatellite loci for Rhododendron ovatum (Ericaceae).

Project description:To estimate the genetic variation of Rhododendron ovatum (Ericaceae), a monoecious evergreen shrub, 23 microsatellite markers were identified from its nuclear genome. We developed 16 polymorphic and seven monomorphic microsatellite primers using the biotin-streptavidin capture method. The 16 polymorphic loci were investigated further using 89 individuals sampled from three populations in China. The number of alleles per locus ranged from four to 30, indicating a high level of polymorphism. The observed heterozygosity varied from 0.1034 to 0.9333, while the expected heterozygosity ranged from 0.1016 to 0.9542. Of these polymorphic primers, 12 were found to be functional in R. simsii, a congeneric species of R. ovatum. Moderate to high levels of genetic variation were found in these microsatellite loci, indicating that they can be applied in future studies of Rhododendron genetic structure, contributing to forest management and conservation.

| S-EPMC5231914 | biostudies-literature

Development and characterization of novel microsatellite loci for Lusitanian toadfish, Halobatrachus didactylus.

Project description:The Lusitanian toadfish Halobatrachus didactylus is an eastern Atlantic polygynous species showing male paternal care. In this paper we describe 5 novel microsatellite loci obtained by 454 GS-FLX Titanium pyrosequencing of a microsatellite-enriched library. The number of alleles per polymorphic locus varied between 2 and 4, and the observed heterozygosity ranged from 0.082 to 0.600. No significant deviation from Hardy-Weinberg equilibrium was found and there was no evidence for linkage disequilibrium. These markers will be of great value for paternity studies and population genetics of this species.

| S-EPMC4304857 | biostudies-literature

Development and characterization of microsatellite loci in the mistletoe Psittacanthus schiedeanus (Loranthaceae).

Project description:Microsatellite primers were developed for the parasitic Psittacanthus schiedeanus, a common mistletoe species on cloud forest-adapted tree hosts in Mesoamerica, to investigate intraspecific genetic patterns of diversity and genetic structure. • Using an enriched library, 10 polymorphic microsatellite loci were developed in P. schiedeanus. All loci consisted of dinucleotide repeats. Average alleles per locus were 12 (4-17), and a total of 120 alleles were recorded across 39 individuals from four populations in Mexico. Primers were tested in 11 additional species, but only amplified successfully in P. calyculatus and P. angustifolius. • The polymorphic loci described will be useful in studies of genetic diversity and genetic population differentiation in natural populations of these parasitic plants, and will provide valuable information to understand the importance of host distribution.

| S-EPMC4298235 | biostudies-literature

Development and characterization of microsatellite loci for smooth cordgrass, Spartina alterniflora (Poaceae).

Project description:Spartina alterniflora is one of the nine most notoriously invasive plants in China. Microsatellite markers were developed for this species to investigate its invasiveness and genetic diversity. • Fifteen polymorphic and seven monomorphic simple sequence repeat (SSR) markers derived from expressed sequence tags (ESTs) were identified and screened in 60 samples of S. alterniflora. The number of alleles per polymorphic locus ranged from two to eight, with an average of 3.8 alleles per polymorphic locus. The expected heterozygosity and observed heterozygosity based on seven disomic loci ranged from 0.27 to 0.46 and 0.21 to 0.51, respectively. The average Shannon index ranged from 0.26 to 0.94 in eight nondisomic loci. • The SSR markers described here may be useful for further investigation of population genetics and invasion dynamics of S. alterniflora.

| S-EPMC4105352 | biostudies-literature

Development and characterization of microsatellite loci for the pseudometallophyte Commelina communis (Commelinaceae).

Project description:• Microsatellite primers were developed for the pseudometallophyte Commelina communis (Commelinaceae), an important pioneer plant for phytoremediation of copper-contaminated soil. Two wild populations collected from metalliferous and nonmetalliferous sites were used to assess the polymorphism at each locus. • Based on the Fast Isolation by AFLP of Sequences COntaining repeats (FIASCO) method, a total of 34 pairs of simple sequence repeat (SSR) markers were designed. When 40 specimens from two populations were screened, 12 microsatellite loci were found to be highly polymorphic. The number of alleles per locus ranged from one to 11 and the observed and expected heterozygosity per locus ranged from 0.000 to 1.000 and from 0.195 to 0.941, respectively. • These markers will be useful for examining genetic diversity, population structure, and gene flow in populations of C. communis under different edaphic conditions and guiding sustainable management plans for phytoremediation.

| S-EPMC4332143 | 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