Microsatellite marker discovery from next-generation sequencing data and subsequent marker characterization in the epizoic barnacle Chelonibia testudinaria (Linnaeus, 1798)

Microsatellite Loci ◽

Model Organisms ◽

Next Generation ◽

Sequencing Data ◽

Genetic Studies ◽

Evolutionary Features ◽

Evolutionary Studies ◽

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 a unusual sexual system, androdioecy. Genetic studies on host specificity and mating behavior are impeded by the lack of fine-scale, highly variable 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.

Microsatellite loci discovery from next-generation sequencing data and marker characterization in the epizoic barnacle Chelonibia testudinaria (Linnaeus, 1798)

10.7287/peerj.preprints.1715v2 ◽

2016 ◽

Author(s):

Christine Ewers-Saucedo ◽

John D Zardus ◽

John P Wares

Keyword(s):

Microsatellite Loci ◽

Model Organisms ◽

Next Generation ◽

Sequencing Data ◽

Genetic Studies ◽

Evolutionary Features ◽

Evolutionary Studies ◽

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 a unusual sexual system, androdioecy. Genetic studies on host specificity and mating behavior are impeded by the lack of fine-scale, highly variable 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.

Microsatellite loci discovery from next-generation sequencing data and marker characterization in the epizoic barnacle Chelonibia testudinaria (Linnaeus, 1798)

10.7287/peerj.preprints.1715 ◽

2016 ◽

Author(s):

Christine Ewers-Saucedo ◽

John D Zardus ◽

John P Wares

Keyword(s):

Microsatellite Loci ◽

Model Organisms ◽

Next Generation ◽

Sequencing Data ◽

Genetic Studies ◽

Evolutionary Features ◽

Evolutionary Studies ◽

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 a unusual sexual system, androdioecy. Genetic studies on host specificity and mating behavior are impeded by the lack of fine-scale, highly variable 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.

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

PeerJ ◽

10.7717/peerj.2019 ◽

2016 ◽

Vol 4 ◽

pp. e2019 ◽

Cited By ~ 5

Author(s):

Christine Ewers-Saucedo ◽

John D. Zardus ◽

John P. Wares

Keyword(s):

Microsatellite Markers ◽

Microsatellite Loci ◽

Model Organisms ◽

Next Generation ◽

Sequencing Data ◽

Genetic Studies ◽

Evolutionary Features ◽

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 barnacleChelonibia testudinaria(Linnaeus, 1758).Chelonibia testudinariaappears 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 onC. testudinaria.

BATCH-GE: Batch analysis of Next-Generation Sequencing data for genome editing assessment

Scientific Reports ◽

10.1038/srep30330 ◽

2016 ◽

Vol 6 (1) ◽

Cited By ~ 46

Author(s):

Annekatrien Boel ◽

Woutert Steyaert ◽

Nina De Rocker ◽

Björn Menten ◽

Bert Callewaert ◽

...

Keyword(s):

Genome Editing ◽

Targeted Mutagenesis ◽

Read Length ◽

Model Organisms ◽

Next Generation ◽

Sequencing Data ◽

Generation Sequencing ◽

Batch Analysis

Abstract Targeted mutagenesis by the CRISPR/Cas9 system is currently revolutionizing genetics. The ease of this technique has enabled genome engineering in-vitro and in a range of model organisms and has pushed experimental dimensions to unprecedented proportions. Due to its tremendous progress in terms of speed, read length, throughput and cost, Next-Generation Sequencing (NGS) has been increasingly used for the analysis of CRISPR/Cas9 genome editing experiments. However, the current tools for genome editing assessment lack flexibility and fall short in the analysis of large amounts of NGS data. Therefore, we designed BATCH-GE, an easy-to-use bioinformatics tool for batch analysis of NGS-generated genome editing data, available from http://. BATCH-GE detects and reports indel mutations and other precise genome editing events and calculates the corresponding mutagenesis efficiencies for a large number of samples in parallel. Furthermore, this new tool provides flexibility by allowing the user to adapt a number of input variables. The performance of BATCH-GE was evaluated in two genome editing experiments, aiming to generate knock-out and knock-in zebrafish mutants. This tool will not only contribute to the evaluation of CRISPR/Cas9-based experiments, but will be of use in any genome editing experiment and has the ability to analyze data from every organism with a sequenced genome.

Faculty Opinions recommendation of VarWalker: personalized mutation network analysis of putative cancer genes from next-generation sequencing data.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.718272765.793499663 ◽

2014 ◽

Author(s):

Gary Bader ◽

Mohamed Helmy

Keyword(s):

Network Analysis ◽

Cancer Genes ◽

Next Generation ◽

Sequencing Data ◽

Faculty Opinions recommendation of Bioinformatory-assisted analysis of next-generation sequencing data for precision medicine in pancreatic cancer.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.727775566.793536095 ◽

2017 ◽

Author(s):

Steve Pereira

Keyword(s):

Pancreatic Cancer ◽

Precision Medicine ◽

Next Generation ◽

Sequencing Data ◽

Assisted Analysis ◽

NGSremix: A software tool for estimating pairwise relatedness between admixed individuals from next-generation sequencing data

G3 Genes|Genome|Genetics ◽

10.1093/g3journal/jkab174 ◽

2021 ◽

Author(s):

Anne Krogh Nøhr ◽

Kristian Hanghøj ◽

Genis Garcia Erill ◽

Zilong Li ◽

Ida Moltke ◽

...

Keyword(s):

Genetic Research ◽

Likelihood Estimation ◽

Software Tool ◽

Estimation Methods ◽

Next Generation ◽

Sequencing Data ◽

Ngs Data ◽

Abstract Estimation of relatedness between pairs of individuals is important in many genetic research areas. When estimating relatedness, it is important to account for admixture if this is present. However, the methods that can account for admixture are all based on genotype data as input, which is a problem for low-depth next-generation sequencing (NGS) data from which genotypes are called with high uncertainty. Here we present a software tool, NGSremix, for maximum likelihood estimation of relatedness between pairs of admixed individuals from low-depth NGS data, which takes the uncertainty of the genotypes into account via genotype likelihoods. Using both simulated and real NGS data for admixed individuals with an average depth of 4x or below we show that our method works well and clearly outperforms all the commonly used state-of-the-art relatedness estimation methods PLINK, KING, relateAdmix, and ngsRelate that all perform quite poorly. Hence, NGSremix is a useful new tool for estimating relatedness in admixed populations from low-depth NGS data. NGSremix is implemented in C/C ++ in a multi-threaded software and is freely available on Github https://github.com/KHanghoj/NGSremix.

recoup: flexible and versatile signal visualization from next generation sequencing

BMC Bioinformatics ◽

10.1186/s12859-020-03902-x ◽

2021 ◽

Vol 22 (1) ◽

Author(s):

Panagiotis Moulos

Keyword(s):

Special Focus ◽

Next Generation ◽

Sequencing Data ◽

User Friendliness ◽

Computational Environment ◽

Level Data ◽

Data Signal ◽

Abstract Background The relentless continuing emergence of new genomic sequencing protocols and the resulting generation of ever larger datasets continue to challenge the meaningful summarization and visualization of the underlying signal generated to answer important qualitative and quantitative biological questions. As a result, the need for novel software able to reliably produce quick, comprehensive, and easily repeatable genomic signal visualizations in a user-friendly manner is rapidly re-emerging. Results recoup is a Bioconductor package for quick, flexible, versatile, and accurate visualization of genomic coverage profiles generated from Next Generation Sequencing data. Coupled with a database of precalculated genomic regions for multiple organisms, recoup offers processing mechanisms for quick, efficient, and multi-level data interrogation with minimal effort, while at the same time creating publication-quality visualizations. Special focus is given on plot reusability, reproducibility, and real-time exploration and formatting options, operations rarely supported in similar visualization tools in a profound way. recoup was assessed using several qualitative user metrics and found to balance the tradeoff between important package features, including speed, visualization quality, overall friendliness, and the reusability of the results with minimal additional calculations. Conclusion While some existing solutions for the comprehensive visualization of NGS data signal offer satisfying results, they are often compromised regarding issues such as effortless tracking of processing and preparation steps under a common computational environment, visualization quality and user friendliness. recoup is a unique package presenting a balanced tradeoff for a combination of assessment criteria while remaining fast and friendly.