Browse
Submit Data
Databases
API
Help

Dataset Information

19 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Isolation and characterization of microsatellite loci for the large-seeded tree Protorhus deflexa (Anacardiaceae).

ABSTRACT: UNLABELLED: PREMISE OF THE STUDY:Protorhus deflexa is an endemic large-seeded tree in Madagascar that depends heavily on insects for cross-pollination and on large-bodied frugivores for seed dispersal. Because such mutualistic relationships are vulnerable to human disturbance, the development of microsatellite markers will enhance analyses of gene flow in this tree species in degraded forests. • METHODS AND RESULTS:Nineteen microsatellite markers were developed for P. deflexa using 454 pyrosequencing. The number of alleles ranged from two to nine, and the ranges of observed and expected heterozygosities were 0.200-0.800 and 0.303-0.821, respectively. The parentage exclusion probability by the 19 loci reached 0.98583 for the first parent and 0.99971 for the second parent. • CONCLUSIONS:These markers will be useful for studying gene flow via pollination and seed dispersal by animals and the genetic structure of P. deflexa in protected and degraded forests in Madagascar.

SUBMITTER: Sato H

PROVIDER: S-EPMC4123381 | biostudies-literature | 2014 Jan

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

Isolation and characterization of microsatellite loci in Pistacia weinmannifolia (Anacardiaceae).

Project description:Fourteen polymorphic microsatellite loci were isolated from the genomic DNA of Pistacia weinmannifolia, using the Fast Isolation by AFLP of Sequences Containing repeats (FIASCO) method, and screened on 12 individuals from each of two wild populations. The 14 polymorphic loci had an average of 4.1 alleles per locus varying from 1 to 9. The observed (H(o)) and expected (H(e)) heterozygosities across the two populations ranged from 0.000 to 0.933 and from 0.000 to 0.906, respectively. Tests for departure from Hardy-Weinberg equilibrium (HWE) and genotypic linkage disequilibrium (LD) were conducted for each of the two populations separately. It was found that no locus significantly deviated from HWE proportions and no significant LD was detected between loci (p < 0.001). In the test of cross-species utility, we successfully amplified nine (64.2%) of 14 loci in P. chinensis and four (28.6%) in P. mexicana. The relatively high level of polymorphism for these markers will facilitate further studies of gene flow, population structure and evolutionary history of P. weinmannifolia and its congeners.

| S-EPMC3233440 | biostudies-literature

Isolation and characterization of polymorphic microsatellite loci in Spondias radlkoferi (Anacardiaceae).

Project description:UNLABELLED: PREMISE OF THE STUDY:Microsatellite markers were developed for Spondias radlkoferi to assess the impact of primate seed dispersal on the genetic diversity and structure of this important tree species of Anacardiaceae. • METHODS AND RESULTS:Fourteen polymorphic loci were isolated from S. radlkoferi through 454 GS-FLX Titanium pyrosequencing of genomic DNA. The number of alleles ranged from three to 12. The observed and expected heterozygosities ranged from 0.382 to 1.00 and from 0.353 to 0.733, respectively. The amplification was also successful in S. mombin and two genera of Anacardiaceae: Rhus aromatica and Toxicodendron radicans. • CONCLUSIONS:These microsatellite loci will be useful to assess the genetic diversity and population structure of S. radlkoferi and related species, and will allow us to investigate the effects of seed dispersal by spider monkeys (Ateles geoffroyi) on the genetic structure and diversity of S. radlkoferi populations in a fragmented rainforest.

| S-EPMC4222547 | biostudies-literature

Isolation and characterization of microsatellite markers for Cotinus coggygria Scop. (Anacardiaceae) by 454 pyrosequencing.

Project description:Cotinus coggygria Scop. (Anacardiaceae) is a deciduous shrub or small tree that is native to a large area covering from southern Europe, east across central Asia, and the Himalayas in northern China. Shotgun 454 pyrosequencing was used to develop microsatellite markers from the genome of C. coggygria. In this study, 349 microsatellite loci were identified from 40,074 individual sequence reads produced by one-sixteenth run, and primer pairs were designed for these loci. To test the primer amplification efficiency, 50 microsatellite primer pairs were tested across 12 individuals from two C. coggygria populations (Wuzhi Mountain: 36°30'N, 113°39'E; Tianlong Mountain: 37°42'N, 112°26'E). Among the 50 tested primer pairs, eight were found to be polymorphic. The average allele number of the microsatellites was 3.5 per locus, with a range from two to five. The inbreeding coefficient ranged from -0.478 to 0.222. The observed and expected heterozygosities varied from 0.167 to 0.750 and from 0.163 to 0.743, respectively. This set of markers is potentially useful for assessing the genetic diversity, as well as for understanding the population structure and phylogeographical and landscape genetic patterns, of C. coggygria.

| S-EPMC6271902 | biostudies-literature

Isolation and characterization of microsatellite loci from Oxytropis diversifolia (Fabaceae).

Project description:Premise of the Study:Microsatellite primers were developed for a perennial legume from northern China, Oxytropis diversifolia (Fabaceae), to investigate population genetic structure of this taxon, as well as potential hybridization events with closely related taxa in this genus. Methods and Results:One hundred and five primer pairs were designed from Illumina sequence data and screened for suitability. Fifteen of these primer pairs were polymorphic, and these primers amplified tri-, tetra-, and pentanucleotide repeats with 10-56 alleles per locus. Cross-amplification tests in three other Oxytropis species from northern China (O. leptophylla, O. neimonggolica, and O. squammulosa) revealed that all of these loci can be amplified successfully and show polymorphism. Conclusions:These primer pairs can be used to assess the genetic diversity and population structure in future studies of O. diversifolia, as well as studies of potential hybridization events with closely related taxa in this genus.

| S-EPMC6055551 | biostudies-literature

Isolation and characterization of microsatellite loci for Smilax sieboldii (Smilacaceae).

Project description:PREMISE OF THE STUDY:Polymorphic microsatellite markers were developed for Smilax sieboldii (Smilacaceae), a member of the S. hispida group with a biogeographic disjunction between eastern Asia and North America, to study the phylogeography and incipient speciation of this species and its close relatives. METHODS AND RESULTS:Transcriptome sequencing produced 47,628 unigenes. Seventeen loci were developed from 122 randomly selected primer pairs. Polymorphism and genetic variation were evaluated for 68 accessions representing five populations of S. sieboldii. The number of alleles per locus ranged from four to 18; the expected heterozygosity ranged from 0.59 to 0.92. Twelve loci were successfully amplified in five related species: S. scobinicaulis, S. californica, S. hispida, S. moranensis, and S. jalapensis. CONCLUSIONS:These novel expressed sequence tag-derived microsatellite markers will facilitate further population genetic research of S. sieboldii and its close allies of the S. hispida group.

| S-EPMC5357126 | biostudies-literature

Isolation and characterization of microsatellite loci from Arthropodium cirratum (Asparagaceae).

Project description:Microsatellite markers were developed for Arthropodium cirratum (Asparagaceae) to study population genetic structure and translocation of this species. These markers were tested for cross-amplification in two other Arthropodium species. Sixteen microsatellite markers were developed from a genomic library and tested in three populations of A. cirratum. The loci exhibited one to five alleles per locus, with private alleles present in each of the populations. Cross-amplification tests in the two other New Zealand Arthropodium species revealed that many of the loci amplify and demonstrate polymorphism in A. bifurcatum. These markers will be useful for determining genetic structure in A. cirratum and for determining the origins of translocated populations of this species.

| S-EPMC5584818 | biostudies-literature

Isolation and characterization of microsatellite loci for Cornus sanguinea (Cornaceae).

Project description:To facilitate genetic and conservation research of Cornus sanguinea, microsatellite loci were isolated and 29 individuals from 11 German populations were genotyped. • Sixteen microsatellite loci were characterized from an enriched small insert genomic library. The number of alleles detected ranged from five to 11 per locus, observed heterozygosity ranged from 0.00 to 1.00, expected heterozygosity ranged from 0.65 to 0.90, and polymorphic information content ranged from 0.59 to 0.88. • The markers described in the study will allow further investigation of population dynamics and the degree of clonal reproduction within populations of C. sanguinea.

| S-EPMC4103144 | biostudies-literature

Isolation and characterization of polymorphic microsatellite loci in Selliera radicans (Goodeniaceae).

Project description:Microsatellite markers were developed for species in the genus Selliera (Goodeniaceae) for future investigations of population genetic structure and interspecific hybridization within the genus. Using 454 pyrosequencing, 15 new markers were developed from microsatellite loci isolated from S. radicans. Primers for the new markers amplify di- and trinucleotide repeat loci from the three Selliera species screened. Ten of the new markers are polymorphic in S. radicans and six of those 10 loci were found to be polymorphic within each congener. For the focal species, S. radicans, the average number of alleles per locus is 3.7 (SE = 0.60) and the average observed and expected heterozygosities are 0.23 (SE = 0.07) and 0.47 (SE = 0.08), respectively. The new markers provide an important resource for future investigations in the genus Selliera for both population genetics and research into hybridization between species.

| S-EPMC4915921 | biostudies-literature

Isolation and characterization of 30 microsatellite loci for Cunninghamia lanceolata (Taxodiaceae).

Project description:To quantify the population-level genetic characteristics of Cunninghamia lanceolata (Taxodiaceae), an important timber conifer, we developed 30 pairs of microsatellite primers based on the nuclear genome. Using the streptavidin-biotin capture system, we developed 14 polymorphic and 16 monomorphic microsatellites. Polymorphisms were detected in 14 loci using 94 individual trees that were collected from three C. lanceolata populations in Hubei and Zhejiang provinces and in Chongqing Municipality, China. There were three to 30 alleles per locus, and the observed and expected heterozygosities ranged from 0.0313-0.8333 and from 0.0313-0.9246, respectively. Cross-species amplification showed that two to seven polymorphic loci were functional in three of the five related species that were collected. Our newly developed microsatellite primers provide neutral molecular markers that are beneficial to future studies of population genetics and germplasm conservation of C. lanceolata.

| S-EPMC5628030 | biostudies-literature

Isolation and characterization of microsatellite loci in Fimbristylis sericea (Cyperaceae)(1.).

Project description:We developed microsatellite markers for Fimbristylis sericea, a coastal herb found in sand dunes in Asia and Australia. • Twelve microsatellite loci were isolated, and the genetic variability within and among local populations was characterized. The number of alleles per locus was two to five with a mean of 3.5, total expected heterozygosity per locus was 0.069-0.645 with a mean of 0.336, and average expected heterozygosity within a population per locus was 0.051-0.230. Most of the loci deviated significantly from Hardy-Weinberg equilibrium. • All 12 microsatellite loci were polymorphic within and among populations. These loci could be useful genetic markers for population genetic studies of F. sericea populations.

| S-EPMC4103114 | 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