ArticlePloS one2015
Validation of Pooled Whole-Genome Re-Sequencing in Arabidopsis lyrata.
Article in PloS one, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 27 papers.
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Who cites it
27 citing papers in PubMed.
- Population genetic variation characterised through serial independent pool-seq: the Cyprus Genome Project.Scientific reports · 2026Article
- Micropropagation of Cannabis sativa: genetic and epigenetic stability assessment over multiple generations.Journal of cannabis research · 2026Article
- Genomic architecture of insertion-deletion (indel) variants in beetal goats of India.Mammalian genome : official journal of the International Mammalian Genome Society · 2026Article
- Genomic implications of the repeated shift to self-fertilization across a species' geographic distribution.The Journal of heredity · 2025Article
- Optimizing genomic diversity assessments for conservation of Bromus auleticus (Trinius ex Nees) using individual and pooled sequencing.PloS one · 2025Article
- Identification of Functional Variants Between Tong Sheep and Hu Sheep by Whole-Genome Sequencing Pools of Individuals.International journal of molecular sciences · 2024Article
- Identification of a Unique Genomic Region in Sweet Chestnut (Plants (Basel, Switzerland) · 2024Article
- Haploid, diploid, and pooled exome capture recapitulate features of biology and paralogy in two non-model tree species.Molecular ecology resources · 2022Article
- Benchmarking the performance of Pool-seq SNP callers using simulated and real sequencing data.Molecular ecology resources · 2021Article
- Growth genes are implicated in the evolutionary divergence of sympatric piscivorous and insectivorous rainbow trout (Oncorhynchus mykiss).BMC ecology and evolution · 2021Article
- Drivers of linkage disequilibrium across a species' geographic range.PLoS genetics · 2021Article
- Article
- Demographic Processes Linked to Genetic Diversity and Positive Selection across a Species' Range.Plant communications · 2020Article
- Shared genetic susceptibilities for irritable bowel syndrome and depressive disorder in Chinese patients uncovered by pooled whole-exome sequencing.Journal of advanced research · 2020Article
- Article
- Population Genomics on the Fly: Recent Advances in Drosophila.Methods in molecular biology (Clifton, N.J.) · 2020Review
- Article
- Accurate Allele Frequencies from Ultra-low Coverage Pool-Seq Samples in Evolve-and-Resequence Experiments.G3 (Bethesda, Md.) · 2019Article
- Comparing Pool-seq, Rapture, and GBS genotyping for inferring weak population structure: The American lobster (Ecology and evolution · 2019Article
- Genomic variation predicts adaptive evolutionary responses better than population bottleneck history.PLoS genetics · 2019Article
Corrections and comments
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Sequencing pooled DNA of multiple individuals from a population instead of sequencing individuals separately has become popular due to its cost-effectiveness and simple wet-lab protocol, although some criticism of this approach remains. Here we validated a protocol for pooled whole-genome re-sequencing (Pool-seq) of Arabidopsis lyrata libraries prepared with low amounts of DNA (1.6 ng per individual). The validation was based on comparing single nucleotide polymorphism (SNP) frequencies obtained by pooling with those obtained by individual-based Genotyping By Sequencing (GBS). Furthermore, we investigated the effect of sample number, sequencing depth per individual and variant caller on population SNP frequency estimates. For Pool-seq data, we compared frequency estimates from two SNP callers, VarScan and Snape; the former employs a frequentist SNP calling approach while the latter uses a Bayesian approach. Results revealed concordance correlation coefficients well above 0.8, confirming that Pool-seq is a valid method for acquiring population-level SNP frequency data. Higher accuracy was achieved by pooling more samples (25 compared to 14) and working with higher sequencing depth (4.1× per individual compared to 1.4× per individual), which increased the concordance correlation coefficient to 0.955. The Bayesian-based SNP caller produced somewhat higher concordance correlation coefficients, particularly at low sequencing depth. We recommend pooling at least 25 individuals combined with sequencing at a depth of 100× to produce satisfactory frequency estimates for common SNPs (minor allele frequency above 0.05).
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