Browse
Submit Data
Databases
API
Help

Dataset Information

10 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Development of 15 microsatellite loci in the endangered Streptanthus glandulosus subsp. niger (Brassicaceae).

ABSTRACT:

Premise of the study

The endangered Streptanthus glandulosus subsp. niger (Brassicaceae) is endemic to a single peninsula in California and threatened by fragmentation. We developed microsatellite markers to investigate genetic diversity in the two extant populations and the degree to which they have diverged from one another.

Methods and results

We used Illumina HiSeq high-throughput sequencing to develop 15 microsatellite markers, 14 of which were polymorphic. These di- and trinucleotide repeats yielded one to 11 alleles per locus in 61 plants across the two populations. Levels of observed and expected heterozygosities ranged from 0.108 to 0.946 and 0.257 to 0.839, respectively. We demonstrated cross-amplification in a second rare subspecies, S. glandulosus subsp. secundus, and in the widespread congener S. tortuosus.

Conclusions

These are the first microsatellites reported for this subspecies, and they will aid in the inclusion of genetic information in conservation planning. Cross-amplification was demonstrated in two related taxa, including one of conservation concern.

SUBMITTER: Swope SM

PROVIDER: S-EPMC6384297 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

Development of microsatellite loci for the endangered seagrass Zostera japonica (Zosteraceae).

Project description:New microsatellite markers were developed for the Asian endangered seagrass Zostera japonica (Zosteraceae) to assess genetic diversity and population structure of this species. In China, Z. japonica populations have drastically decreased since the 1970s. A total of 12 polymorphic tetranucleotide microsatellite loci were isolated and characterized in Z. japonica. The number of alleles per locus ranged from one to 11. The expected and observed heterozygosity ranged from 0 to 0.772 and from 0 to 1.000, respectively. The new microsatellites will be useful in evaluating clonality and population structure of Z. japonica and aiding in conservation and management of the endangered seagrass in Asia.

| S-EPMC4578380 | biostudies-literature

Development and characterization of microsatellite loci in the endangered species Taxus wallichiana (Taxaceae).

Project description:Microsatellite primers were developed in the endangered tree species Taxus wallichiana from Nepal to investigate regional genetic differentiation, local genetic diversity, and gene flow for the conservation of this species under climate- and land-use change scenarios in mountain regions of Nepal. • We developed 10 highly polymorphic microsatellite markers from 454 DNA sequencing. Characterization of the new microsatellite loci was done in 99 individuals collected from three valleys with different climatic regimes. The number of alleles per locus varied from four to 12. Observed heterozygosity of populations, averaged across loci, ranged from 0.30 to 0.59. • The new markers provided by this study will substantially increase the resolution for detailed studies in phylogeography, population genetics, and parentage analysis.

| S-EPMC4105282 | biostudies-literature

Development of 12 polymorphic microsatellite loci for the endangered Seychelles palm Lodoicea maldivica (Arecaceae).

Project description:PREMISE OF THE STUDY:The evolutionarily and ecologically distinct coco de mer palm Lodoicea maldivica (Arecaceae) is endemic to two islands in the Seychelles. Before colonization of the islands by man, the endangered palm formed large monodominant stands, but its natural range is now restricted to four main populations and several patches of isolated individuals. Microsatellite markers were designed to investigate the genetic structure of the remaining natural populations of L. maldivica. METHODS AND RESULTS:We developed 12 polymorphic and three monomorphic microsatellite markers for this species, with a mean number of alleles per locus of 13.2 (range 5-21) and expected heterozygosity values ranging from 0.31-0.91 for the polymorphic loci. CONCLUSIONS:These markers enable us to study the patterns of genetic diversity, contemporary seed dispersal, and the fine-scale spatial genetic structure of this important conservation flagship species.

| S-EPMC4850054 | biostudies-literature

Development and characterization of microsatellite loci for the endangered scrub lupine, Lupinus aridorum (Fabaceae).

Project description:Microsatellite primers were developed in scrub lupine (Lupinus aridorum, Fabaceae), an endemic species to Florida that is listed as endangered in the United States, to assess connectivity among populations, identify hybrids, and examine genetic diversity. We isolated and characterized 12 microsatellite loci polymorphic in scrub lupine or in closely related species (i.e., sky-blue lupine [L. diffusus] and Gulf Coast lupine [L. westianus]). Loci showed low to moderate polymorphism, ranging from two to 14 alleles per locus and 0.01 to 0.86 observed heterozygosity. These loci are the first developed for Florida species of lupine and will be used to determine differentiation among species and to aid in conservation of the endangered scrub lupine.

| S-EPMC4406839 | biostudies-literature

Development of 22 polymorphic microsatellite loci for the critically endangered Morato's Digger Toad, Proceratophrys moratoi.

Project description:The Morato's digger toad (Proceratophrys moratoi) inhabits Brazilian moist savannas and is critically endangered due to its very limited geographic distribution, reduced number of isolated populations, and evidence of population decline and local extinctions. With the objective of providing tools for the genetic study of the species, 22 polymorphic microsatellite loci were isolated and screened using DNA extracted from samples of oral mucosa cells obtained from 113 individuals representing five remnant P. moratoi populations in the Brazilian state of São Paulo. These markers presented 2-18 alleles per locus, polymorphism information content (PIC) of 0.02-0.87, observed heterozygosity of 0.02-0.96 and expected heterozygosity of 0.02-0.87. Three of the loci deviated significantly from Hardy-Weinberg equilibrium in one of the populations, possibly due to the presence of null alleles. Significant linkage disequilibrium was also detected between three pairs of loci. The molecular markers developed in this study were able to discriminate each of the individuals sampled (identity analysis). This means that they will be extremely useful for future genetic studies applied to the conservation of P. moratoi, providing a baseline for estimating the levels of genetic diversity, pedigrees, inbreeding, and population structure, which will be essential for the development of effective genetic management programs.

| S-EPMC3497271 | biostudies-literature

Development and characterization of microsatellite loci for the Moroccan endemic endangered species Argania spinosa (Sapotaceae).

Project description:Microsatellite loci were developed for the Moroccan endemic endangered species Argania spinosa with a combination of a typical library enrichment procedure and a 454 GS FLX Titanium-based high-throughput sequencing approach. • A genomic DNA library was enriched and further screened using (GA)15, (GTA)8, and (TTC)8 biotin-labeled probes coupled with chemi-luminescence detection. To increase simple sequence repeat (SSR) loci number, an ultra-high-throughput sequencing-based approach was used. Evaluation of all primer pairs was performed with labeled dUTP on an ABI 3130xl sequencer. Eleven polymorphic SSR loci were selected out of 79 SSR regions and extensively characterized on 150 individuals from eight populations. Total alleles ranged from six to 19 alleles per locus while expected heterozygosity ranged from 0.618 to 0.869. • The SSRs developed here will be used to further characterize the genetic diversity of A. spinosa across its distribution range, mainly in the southern part of Morocco and southwestern Algeria. They may also be transferable to other Sapotaceae species.

| S-EPMC4103133 | biostudies-literature

Development of 11 microsatellite loci for an endangered herb, Paraisometrum mileense (Gesneriaceae), in southwest China.

Project description:Microsatellite markers were developed to investigate the genetic diversity and population structure of the endangered species Paraisometrum mileense, as well as its evolutionary history. • Using the Fast Isolation by AFLP of Sequences COntaining repeats (FIASCO) protocol, 11 polymorphic primer sets were obtained in P. mileense. The number of alleles per locus ranged from one to nine with an average 3.8, and the observed and expected heterozygosities ranged from 0 to 1 and 0 to 0.89, respectively, for the available three populations. • These markers may be useful for further investigation of the conservation genetics of P. mileense.

| S-EPMC4105348 | biostudies-literature

Development of nine markers and characterization of the microsatellite loci in the endangered Gymnogobius isaza (Gobiidae).

Project description:Gymnogobius isaza is a freshwater goby endemic to Lake Biwa, Japan. They experienced a drastic demographic bottleneck in the 1950s and 1980s and slightly recovered thereafter, but the population size is still very small. To reveal dynamics of genetic diversity of G. isaza, we developed nine microsatellite markers based on the sequence data of a related goby Chaenogobius annularis. Nine SSR (Simple Sequence Repeats) markers were successfully amplified for raw and formalin-fixed fish samples. The number of alleles and expected heterozygosities ranged from one to 10 and from 0.06 to 0.84, respectively, for the current samples, while one to 12 and 0.09 to 0.83 for historical samples. The markers described here will be useful for investigating the genetic diversity and gene flow and for conservation of G. isaza.

| S-EPMC3382742 | biostudies-literature

Microsatellite loci in the Gypsophyte Lepidium subulatum (Brassicaceae), and transferability to other Lepidieae.

Project description:Polymorphic microsatellite markers were developed for the Ibero-North African, strict gypsophyte Lepidium subulatum to unravel the effects of habitat fragmentation in levels of genetic diversity, genetic structure and gene flow among its populations. Using 454 pyrosequencing 12 microsatellite loci including di- and tri-nucleotide repeats were characterized in L. subulatum. They amplified a total of 80 alleles (2-12 alleles per locus) in a sample of 35 individuals of L. subulatum, showing relatively high levels of genetic diversity, H(O) = 0.645, H(E) = 0.627. Cross-species transferability of all 12 loci was successful for the Iberian endemics Lepidium cardamines, Lepidium stylatum, and the widespread, Lepidium graminifolium and one species each of two related genera, Cardaria draba and Coronopus didymus. These microsatellite primers will be useful to investigate genetic diversity, population structure and to address conservation genetics in species of Lepidium.

| S-EPMC3472779 | biostudies-literature

Isolation and characterization of microsatellite loci for the endangered wetland plant Adenophora palustris (Campanulaceae).

Project description:Adenophora palustris (Campanulaceae) is an endangered wetland plant species in Japan. Although it is widely distributed in East Asia, only six extant populations are known in Japan, with fewer than 1000 individuals in total. We developed 15 microsatellite markers for this species and confirmed their utility for the closely related species A. triphylla var. japonica. Ten polymorphic loci were characterized for genetic variation within three populations of A. palustris. The number of alleles per locus ranged from four to 15, with an average of 9.3; the expected heterozygosity ranged from 0.48 to 0.89, with an average of 0.74. Nine loci were successfully amplified in A. triphylla var. japonica, and three of these loci showed polymorphism. These markers are useful for investigating genetic diversity and gene flow within and among remnant populations of A. palustris in Japan, and the results will provide crucial information for conservation.

| S-EPMC5033367 | 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