STRyper: A macOS application for microsatellite genotyping and chromatogram management

PLoS ONE, Journal Year: 2025, Volume and Issue: 20(2), P. e0318806 - e0318806

Published: Feb. 20, 2025

Microsatellite markers analyzed by capillary sequencing remain useful tools for rapid genotyping and low-cost studies. This contrasts with the lack of a free application to analyze chromatograms microsatellite that is not restricted human genotyping. To fill this gap, I have developed STRyper, macOS whose source code published under General Public License. STRyper only uses libraries, making it very lightweight, responsive, behaving like modern application. Its three-pane window enables easy management viewing imported from FSA HID files, creation size standards marker panels (including bins). features powerful search capabilities (with smart folders) graphical user interface allowing, among others, manual correction DNA ladders individual genotypes drag-and-drop. It also introduces new way mitigate effect variations in electrophoretic conditions on estimated allele sizes.

Language: Английский

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Development of a Genotyping‐in‐Thousands by Sequencing (GT‐Seq) Panel for Identifying Individuals and Estimating Relatedness Among Alaska Black Bears (Ursus americanus)

Ecology and Evolution, Journal Year: 2025, Volume and Issue: 15(4)

Published: April 1, 2025

The management and conservation of large mammals, such as black bears (Ursus americanus), have long been informed by genetic estimates population size individual dispersal. Amplicon sequencing methods, also known 'genotyping-in-thousands-by sequencing' (GT-seq), now enable the efficient cost-effective genotyping hundreds loci individuals in same run. Here, we develop a GT-seq panel for identification kinship inference Alaska bears. Using genomic data from restriction site-associated DNA hunter-harvested Southcentral (n = 85), identified 170 microhaplotype single nucleotide polymorphism (SNP) that were highly heterozygous local populations. To sexing individuals, included previously published sex-linked locus panel. We empirically validated using samples collected at different spatial scales. These tissues 82) obtained within small geographic area Anchorage, Alaska, which likely to be relatives well geographically widespread locations throughout Alaska. Empirical validation indicated high success genotype reproducibility across replicate subsamples. Computer simulations demonstrated had ample statistical power distinguishing distinct first-order (parent-offspring full-sibling pairs) unrelated individuals. As final proof concept, was used identify close kin sampled urban wild habitats anticipate will useful resource monitoring bear

Language: Английский

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Beyond Presence and Absence: Using eDNA and Microsatellite Genotyping to Estimate Densities of Microscopic Life Forms in Wild Populations

Molecular Ecology Resources, Journal Year: 2025, Volume and Issue: unknown

Published: May 2, 2025

ABSTRACT Many challenges arise when monitoring organisms with cryptic life‐histories. For example, some life‐stages are hard to identify or sample due their microscopic nature, which creates unknowns surrounding an organism's population dynamics. Environmental DNA (eDNA) is a non‐invasive sampling technique used monitor species traditional survey methods challenging. Generally, eDNA has been quantify the presence/absence of in various habitats. However, recent advances high‐throughput amplicon sequencing techniques have enabled researchers detect intraspecific genetic diversity eDNA. In this study, we present two complementary R packages that can be estimate number individuals sample. The first package (Amplicomsat) cleans microsatellite sequences and counts observed alleles identified Our second (GenotypeQuant) then uses numerical maximum likelihood estimator (NMLE) contributors most likely produced sequenced panel amplified from We simulations characterise accuracy precision method. estimated densities Nereocystis luetkeana (bull kelp) gametophytes collected experiment manipulated gametophytes. Finally, analysed benthic kelp forest found gametophyte estimates by NMLE varied within +3/−2 processing rocks 8 seeded 500 800 gametophytes·m −2 July, five more months since spore germination before current year's release. Gametophyte abundance scaled area numbers were higher than total sporophyte densities.

Language: Английский

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Environmental effects on faecal genotyping success in mesocarnivores

Conservation Genetics Resources, Journal Year: 2024, Volume and Issue: 16(4), P. 307 - 319

Published: July 1, 2024

Abstract Non-invasive genetic sampling can be used in research, monitoring, and conservation of wild animals to, for example, provide insights into diets, identify individuals estimate population sizes. may especially useful to monitor elusive species because DNA derived from materials such as hairs faeces without handling individuals. However, the reliability results this technique is dependent on quality obtained samples, which deteriorate exposure environmental conditions sample age. While freshness an important factor, combined effect different field genotyping success not fully understood. To address gap, we systematically investigated effects age faeces, experimental setting four treatments that rain temperature typical central European climates. We compared performance a microsatellite marker set SNP panel red fox ( Vulpes vulpes ), well pine marten Martes martes ) resampled over 21 days. found decreased significantly with age, however did impact success. Furthermore, SNPs amplified more successfully time than respective microsatellites. Therefore, use instead conventional microsatellites, when using faecal samples analysis relying correct amplifications, could advantageous. recommend prioritise collection fresh regardless conditions.

Language: Английский

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MhGeneS: An Analytical Pipeline to Allow for Robust Microhaplotype Genotyping

Molecular Ecology Resources, Journal Year: 2024, Volume and Issue: unknown

Published: Oct. 4, 2024

ABSTRACT Microhaplotypes are small linked genomic regions comprising two or more single‐nucleotide polymorphisms (SNPs) that being applied in forensics and emerging wildlife monitoring studies epidemiology. Typically, targeted non‐coding regions, microhaplotypes exonic can be designed with larger amplicons to capture functional non‐synonymous sites minimise insertion/deletion (indel) polymorphisms. Quality control is an important first step for high‐confidence genotyping counteract such false‐positive variants. As genetic markers higher polymorphism compared biallelic SNPs, it critical ensure sequencing errors across the microhaplotype amplicon filtered out avoid introducing false‐haplotypes. We developed MhGeneS pipeline which works tandem Seq2Sat help validate of coding region genes, broader applicability any profiling. genotyped Zfx (≅ 160 bp) Zfy 140 as well exon prion protein ( Prnp ) gene 370 caribou Rangifer tarandus using paired‐end Illumina technology. quality metrics affecting calling, we identified error rate profile related overlap non‐overlap reads read depth significant. In case , achieved confident calling through by removing sections 5′ 3′ a minimum 20. Read sequence trimming may locus‐specific, validation these parameters recommended before high‐throughput profiling samples.

Language: Английский

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