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18 results for “Pool-Seq”
GDS file for Pool-Seq object -- DEST + VA data
<p>See https://github.com/Jcbnunez/Cville-Seasonality-2016-2019</p>
Data for: SNPs detected in pool-seq data from resistant and susceptible Cimex lectularius populations
<p>In the last few years, the bed bug <em>Cimex lectularius</em> has been an increasing problem world-wide, mainly due to the development of insecticide resistance to pyrethroids. The characterization of resistance alleles is a prerequisite to improve surveillance and resistance management. To identify genomic variants associated with pyrethroid resistance in <em>Cimex lectularius</em>, we compared the genetic composition of two recent and resistant populations with that of two ancientsusceptible strains using a genome-wide pool-seq design. We identified a large 6 Mb "superlocus" showing particularly high genetic differentiation and association with the resistance phenotype. This superlocus contained several clustered resistance genes, andwas also characterized by a high density of structural variants (inversions, duplications). The possibility that this superlocus constitute a resistance "supergene" that evolved after the clustering of alleles adapted to insecticide and after reduction in recombination is discussed.</p>
Data for: SNPs detected in pool-seq data from resistant and susceptible Cimex lectularius populations
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Data from: Exploring a Pool-seq only approach for gaining population genomic insights in non-model species
<p>Developing genomic insights is challenging in non-model species for which resources are often scarce and prohibitively costly. Here, we explore the potential of a recently established approach using Pool-seq data to generate a de novo genome assembly for mining exons, upon which Pool-seq data is used to estimate population divergence and diversity. We do this for two pairs of sympatric populations of brown trout (Salmo trutta); one naturally sympatric set of populations and another pair of populations introduced to a common environment. We validate our approach by comparing the results to those from markers previously used to describe the populations (allozymes and individual based SNPs) and from mapping the Pool-seq data to a reference genome of the closely related Atlantic salmon (Salmo salar). We find that genomic differentiation (FST) between the two introduced populations exceeds that of the naturally sympatric populations (FST = 0.13 and 0.03 between the introduced and the naturally sympatric populations, respectively), in concordance with estimates from the previously used SNPs. The same level of population divergence is found for the two genome assemblies but estimates of average genic diversity differ (π ≈0.002 and π ≈0.001 when mapping to S. trutta and S. salar, respectively), although the relationships between population values are largely consistent. This discrepancy might be attributed to biases when mapping to a haploid condensed assembly made of highly fragmented read data compared to using a high-quality reference assembly from a divergent species. We conclude that the Pool-seq only approach can be suitable for detecting and quantifying genome wide population differentiation, and for comparing genomic diversity in populations of non-model species where reference genomes are lacking.</p>
Data from: Adaptive genomic divergence under high gene flow between freshwater and brackish-water ecotypes of prickly sculpin (Cottus asper) revealed by Pool-Seq
Understanding the genomic basis of adaptive divergence in the presence of gene flow remains a major challenge in evolutionary biology. In prickly sculpin (Cottus asper), an abundant euryhaline fish in northwestern North America, high genetic connectivity among brackish-water (estuarine) and freshwater (tributary) habitats of coastal rivers does not preclude the build-up of neutral genetic differentiation and emergence of different life history strategies. Because these two habitats present different osmotic niches, we predicted high genetic differentiation at known teleost candidate genes underlying salinity tolerance and osmoregulation. We applied whole-genome sequencing of pooled DNA samples (Pool-Seq) to explore adaptive divergence between two estuarine and two tributary habitats. Paired-end sequence reads were mapped against genomic contigs of European Cottus, and the gene content of candidate regions was explored based on comparisons with the threespine stickleback genome. Genes showing signals of repeated differentiation among brackish-water and freshwater habitats included functions such as ion transport and structural permeability in freshwater gills, which suggests that local adaptation to different osmotic niches might contribute to genomic divergence among habitats. Overall, the presence of both repeated and unique signatures of differentiation across many loci scattered throughout the genome is consistent with polygenic adaptation from standing genetic variation and locally variable selection pressures in the early stages of life history divergence.
Data from: Adaptive genomic divergence under high gene flow between freshwater and brackish-water ecotypes of prickly sculpin (Cottus asper) revealed by Pool-Seq
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Data from: A new method for studying population genetics of cyst nematodes based on Pool-Seq and genome-wide allele frequency analysis
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Data from: Exploring a Pool-seq only approach for gaining population genomic insights in non-model species
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Data from: Using Pool-seq to search for genomic regions affected by hybrid inviability in the copepod T. californicus
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Data from: The impact of library preparation protocols on the accuracy of allele frequency estimates in Pool-Seq data
Sequencing pools of individuals (Pool-Seq) is a cost-effective method to determine genome-wide allele frequency estimates. Given the importance of meta-analyses combining data sets, we determined the influence of different genomic library preparation protocols on the consistency of allele frequency estimates. We found that typically no more than 1% of the variation in allele frequency estimates could be attributed to differences in library preparation. Also read length had only a minor effect on the consistency of allele frequency estimates. By far, the most pronounced influence could be attributed to sequence coverage. Increasing the coverage from 30- to 50-fold improved the consistency of allele frequency estimates by at least 27%. We conclude that Pool-Seq data can be easily combined across different library preparation methods, but sufficient sequence coverage is key to reliable results.
Data from: Suitability of different mapping algorithms for genome-wide polymorphism scans with Pool-Seq data.
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Data from: The impact of library preparation protocols on the accuracy of allele frequency estimates in Pool-Seq data
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Data from: Inference of chromosomal inversion dynamics from Pool-Seq data in natural and laboratory populations of Drosophila melanogaster
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3’Pool-seq: an optimized cost-efficient and scalable method of whole-transcriptome gene expression profiling (Glitazone)
GEO Series GSE125570. Homo sapiens. 80 samples. Type: Expression profiling by high throughput sequencing.
3’Pool-seq: an optimized cost-efficient and scalable method of whole-transcriptome gene expression profiling (Run0050)
GEO Series GSE125568. Mus musculus. 24 samples. Type: Expression profiling by high throughput sequencing.
3’Pool-seq: an optimized cost-efficient and scalable method of whole-transcriptome gene expression profiling (Run0064)
GEO Series GSE125569. Mus musculus. 32 samples. Type: Expression profiling by high throughput sequencing.
3’Pool-seq: an optimized cost-efficient and scalable method of whole-transcriptome gene expression profiling (Run0004)
GEO Series GSE125567. Mus musculus. 6 samples. Type: Expression profiling by high throughput sequencing.
3’Pool-seq: an optimized cost-efficient and scalable method of whole-transcriptome gene expression profiling
GEO Series GSE125571. Homo sapiens; Mus musculus. 142 samples. Type: Expression profiling by high throughput sequencing.
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