Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Microsatellite loci discovery from next-generation sequencing data and loci characterization in the epizoic barnacle Chelonibia testudinaria (Linnaeus, 1758).

ABSTRACT: Microsatellite markers remain an important tool for ecological and evolutionary research, but are unavailable for many non-model organisms. One such organism with rare ecological and evolutionary features is the epizoic barnacle Chelonibia testudinaria (Linnaeus, 1758). Chelonibia testudinaria appears to be a host generalist, and has an unusual sexual system, androdioecy. Genetic studies on host specificity and mating behavior are impeded by the lack of fine-scale, highly variable markers, such as microsatellite markers. In the present study, we discovered thousands of new microsatellite loci from next-generation sequencing data, and characterized 12 loci thoroughly. We conclude that 11 of these loci will be useful markers in future ecological and evolutionary studies on C. testudinaria.

SUBMITTER: Ewers-Saucedo C

PROVIDER: S-EPMC4878368 | biostudies-literature | 2016

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Microsatellite loci discovery from next-generation sequencing data and loci characterization in the epizoic barnacle Chelonibia testudinaria (Linnaeus, 1758).

Ewers-Saucedo Christine C Zardus John D JD Wares John P JP

PeerJ 20160517

Microsatellite markers remain an important tool for ecological and evolutionary research, but are unavailable for many non-model organisms. One such organism with rare ecological and evolutionary features is the epizoic barnacle Chelonibia testudinaria (Linnaeus, 1758). Chelonibia testudinaria appears to be a host generalist, and has an unusual sexual system, androdioecy. Genetic studies on host specificity and mating behavior are impeded by the lack of fine-scale, highly variable markers, such ...[more]

PMID: 27231653

Similar Datasets

Development and characterization of 26 novel microsatellite loci for the trochid gastropod Gibbula divaricata (Linnaeus, 1758), using Illumina MiSeq next generation sequencing technology.

Project description:In the present study we used the high-throughput sequencing technology Illumina MiSeq to develop 26 polymorphic microsatellite loci for the marine snail Gibbula divaricata. Four to 32 alleles were detected per locus across 30 samples analyzed. Observed and expected heterozygosities ranged from 0.130 to 0.933 and from 0.294 to 0.956, respectively. No significant linkage disequilibrium existed. Seven loci deviated from Hardy-Weinberg equilibrium that could not totally be explained by the presence of null alleles. Sympatric distribution with other species of the genus Gibbula, as G. rarilineata and G. varia, lead us to test the cross utility of the developed markers in these two species, which could be useful to test common biogeographic patterns or potential hybridization phenomena, since morphological intermediate specimens were found.

| S-EPMC4811169 | biostudies-literature

The complete mitochondrial genome of rubble crab <i>Daldorfia horrida</i> (Linnaeus, 1758) using next-generation sequencing.

Project description:In this study, the complete mitochondrial genome of the rubble carb Daldorfia horrida was determined using Illumina next-generation sequencing. The circular mitogenome is 15,737?bp, with 13 protein-coding genes (PCGs), 22 tRNA genes, two rRNA genes and one control region. The base composition is significantly biased (A, G, T, and C was 35.5%, 10.2%, 34.9%, and 19.4%, respectively) with A?+?T contents of 70.4%. Five microsatellites were identified in the mitogenome located in ND1, ND4, 16S genes and D-loop region. Phylogenetic tree showed that D. horrida is first clustered with Pseudocarcinus gigas and Myomenippe fornasinii, which revealed that Parthenopoidea has a close affinity with Eriphioidea in Heterotremata.

| S-EPMC7707263 | biostudies-literature

Complete mitochondrial genome of the Northern Long-eared Owl (<i>Asio otus</i> Linnaeus, 1758) determined using next-generation sequencing.

Project description:In this study, the mitogenome of Asio otus, the Northern Long-eared Owl, was analysed using Illumina next-generation sequencing. The mitogenome was found to be a circular molecule, 17,735?bp long with a slight AT bias (53.0%). The gene arrangement pattern was the same as that of a typical vertebrate, containing 37 genes (13 protein-coding genes (PCGs), 22 transfer RNA genes, two ribosomal RNA genes, and a non-coding control region). In the putative control region (1984?bp), there were two types of tandem repeats at the end of the region. A phylogenetic tree was constructed using the 13 PCG sequences discovered in this study and those of that have been previously published of other Strigidae species and revealed a close relationship between A. otus and A. flammeus. The newly generated mitogenome from this study enriches the genomic resources available for future evolutionary studies and promotes conservation genetics of this species.

| S-EPMC7800783 | biostudies-literature

Identification and Characterization of Microsatellite Loci in Maqui (Aristotelia chilensis [Molina] Stunz) Using Next-Generation Sequencing (NGS).

Project description:Maqui (Aristotelia chilensis [Molina] Stunz) is a small dioecious tree native to South America with edible fruit characterized by very high antioxidant capacity and anthocyanin content. To preserve maqui as a genetic resource it is essential to study its genetic diversity. However, the complete genome is unknown and only a few gene sequences are available in databases. Simple sequence repeats (SSR) markers, which are neutral, co-dominant, reproducible and highly variable, are desirable to support genetic studies in maqui populations. By means of identification and characterization of microsatellite loci from a maqui genotype, using 454 sequencing technology, we develop a set of SSR for this species. Obtaining a total of 165,043 shotgun genome sequences, with an average read length of 387 bases, we covered 64 Mb of the maqui genome. Reads were assembled into 4,832 contigs, while 98,546 reads remained as singletons, generating a total of 103,378 consensus genomic sequences. A total of 24,494 SSR maqui markers were identified. Of them, 15,950 SSR maqui markers were classified as perfects. The most common SSR motifs were dinucleotide (31%), followed by tetranucleotide (26%) and trinucleotide motifs (24%). The motif AG/CT (28.4%) was the most abundant, while the motif AC (89 bp) was the largest. Eleven polymorphic SSRs were selected and used to analyze a population of 40 maqui genotypes. Polymorphism information content (PIC) ranged from 0.117 to 0.82, with an average of 0.58. Non-significant groups were observed in the maqui population, showing a panmictic genetic structure. In addition, we also predicted 11150 putative genes and 3 microRNAs (miRNAs) in maqui sequences. This results, including partial sequences of genes, some miRNAs and SSR markers from high throughput next generation sequencing (NGS) of maqui genomic DNA, constitute the first platform to undertake genetic and molecular studies of this important species.

| S-EPMC4961369 | biostudies-literature

Isolation of Microsatellite Loci by Next-Generation Sequencing of the Critically Endangered Northern Bald Ibis, Geronticus eremita.

Project description:The Northern Bald Ibis is one of the rarest bird species, extinct in Europe for 400 years and critically endangered worldwide. The European Union-co-financed LIFE+ project "Reason for Hope - Reintroduction of the Northern Bald Ibis in Europe" aims to reintroduce the species in Europe (Germany, Austria, Italy). In order to obtain information on the genetic diversity within zoo colonies and the reintroduced population, 15 polymorphic microsatellite markers, specific for the Northern Bald Ibis, Geronticus eremita (Linnaeus, 1785), have been isolated from next-generation sequencing (Illumina MiSeq) and are described here. The microsatellite primers were tested in 30 individuals and measures of genetic variability were calculated. Values for the observed heterozygosity ranged from 0.393 to 0.867, while expected heterozygosity ranged from 0.573 to 0.718. Ten out of 15 loci were in Hardy-Weinberg equilibrium and only one showed indication for the presence of null alleles. The newly developed PCR primers can be used to examine population genetic parameters, e.g. for future conservation genetic studies of this critically endangered bird species.

| S-EPMC4888436 | biostudies-literature

Oryzaephilus surinamensis strain:Linnaeus,1758

Project description:Oryzaephilus surinamensis strain:Linnaeus,1758 Genome sequencing and assembly

| PRJNA808116 | ENA

Crepidula fornicata strain:Linnaeus 1758

Project description:Crepidula fornicata (Linnaeus 1758) sequencing project

| PRJNA46697 | ENA

Applicability of next generation sequencing technology in microsatellite instability testing.

Project description:Microsatellite instability (MSI) is a useful marker for risk assessment, prediction of chemotherapy responsiveness and prognosis in patients with colorectal cancer. Here, we describe a next generation sequencing approach for MSI testing using the MiSeq platform. Different from other MSI capturing strategies that are based on targeted gene capture, we utilize "deep resequencing", where we focus the sequencing on only the microsatellite regions of interest. We sequenced a series of 44 colorectal tumours with normal controls for five MSI loci (BAT25, BAT26, BAT34c4, D18S55, D5S346) and a second series of six colorectal tumours (no control) with two mononucleotide loci (BAT25, BAT26). In the first series, we were able to determine 17 MSI-High, 1 MSI-Low and 26 microsatellite stable (MSS) tumours. In the second series, there were three MSI-High and three MSS tumours. Although there was some variation within individual markers, this NGS method produced the same overall MSI status for each tumour, as obtained with the traditional multiplex PCR-based method.

| S-EPMC4377833 | biostudies-other

Cryopreservation of lumpfish Cyclopterus lumpus (Linnaeus, 1758) milt.

Project description:This study has established a successful protocol to cryopreserve lumpfish Cyclopterus lumpus (Linnaeus, 1758) milt. Three cryosolutions were tested based on Mounib's medium; the original medium including reduced l-glutathione (GSH), the basic sucrose and potassium bicarbonate medium without GSH, or with hen's egg yolk (EY). Dimethyl sulphoxide (DMSO) was used as the cryoprotectant along with all three diluents in a 1-2 dilution. Cryopreservation was performed with the mentioned cryosolutions at two freezing rates. Motility percentages of spermatozoa were evaluated using ImageJ with a computer assisted sperm analyzer (CASA) plug-in. Findings revealed that spermatozoa cryopreserved in Mounib's medium without GSH had a post-thaw motility score of 6.4 percentage points (pp) higher than those in the original Mounib's medium, and an addition of EY to the modified Mounib's medium lowered the post-thaw motility score by 19.3 pp. The difference in motility between both freezing rates was 13.0 pp, and samples cryopreserved on a 4.8 cm high tray resulted in a better post-thaw motility score. On average, cryopreserved milt had a 24.1 pp lower post-thaw motility score than fresh milt. There was no significant difference in fertilisation success between cryopreserved and fresh milt. Cryopreservation of lumpfish milt has, to our knowledge, never been successfully carried out before. The established protocol will be a main contributing factor in a stable production of lumpfish juveniles in future.

| S-EPMC4458125 | biostudies-literature

Efficiency to Discovery Transgenic Loci in GM Rice Using Next Generation Sequencing Whole Genome Re-sequencing.

Project description:Molecular characterization technology in genetically modified organisms, in addition to how transgenic biotechnologies are developed now require full transparency to assess the risk to living modified and non-modified organisms. Next generation sequencing (NGS) methodology is suggested as an effective means in genome characterization and detection of transgenic insertion locations. In the present study, we applied NGS to insert transgenic loci, specifically the epidermal growth factor (EGF) in genetically modified rice cells. A total of 29.3 Gb (~72× coverage) was sequenced with a 2 × 150 bp paired end method by Illumina HiSeq2500, which was consecutively mapped to the rice genome and T-vector sequence. The compatible pairs of reads were successfully mapped to 10 loci on the rice chromosome and vector sequences were validated to the insertion location by polymerase chain reaction (PCR) amplification. The EGF transgenic site was confirmed only on chromosome 4 by PCR. Results of this study demonstrated the success of NGS data to characterize the rice genome. Bioinformatics analyses must be developed in association with NGS data to identify highly accurate transgenic sites.

| S-EPMC4623445 | 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