ArticleGenome biology and evolution2009
Population genomic inferences from sparse high-throughput sequencing of two populations of Drosophila melanogaster.
Article in Genome biology and evolution, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 41 papers.
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Who cites it
41 citing papers in PubMed.
- Transposable elements as drivers of genome evolution in Drosophila virilis.Nucleic acids research · 2026Article
- Local assembly of long reads enables phylogenomics of transposable elements in a polyploid cell line.Nucleic acids research · 2022Article
- Ongoing transposition in cell culture reveals the phylogeny of diverse Drosophila S2 sublines.Genetics · 2022Article
- Regulatory regions in natural transposable element insertions drive interindividual differences in response to immune challenges in Drosophila.Genome biology · 2021Article
- Transposable Element Landscape in Drosophila Populations Selected for Longevity.Genome biology and evolution · 2021Article
- Evolution of genome structure in theGenome research · 2021Article
- Telomeric TART elements target the piRNA machinery in Drosophila.PLoS biology · 2020Article
- Nanopore sequencing and Hi-C scaffolding provide insight into the evolutionary dynamics of transposable elements and piRNA production in wild strains of Drosophila melanogaster.Nucleic acids research · 2020Article
- Population Genomics on the Fly: Recent Advances in Drosophila.Methods in molecular biology (Clifton, N.J.) · 2020Review
- The Genome of Drosophila innubila Reveals Lineage-Specific Patterns of Selection in Immune Genes.Molecular biology and evolution · 2019Article
- Conserved Noncoding Elements Influence the Transposable Element Landscape in Drosophila.Genome biology and evolution · 2018Article
- McClintock: An Integrated Pipeline for Detecting Transposable Element Insertions in Whole-Genome Shotgun Sequencing Data.G3 (Bethesda, Md.) · 2017Article
- The landscape of extreme genomic variation in the highly adaptable Atlantic killifish.Genome biology and evolution · 2017Article
- Molecular Population Genetics.Genetics · 2017Review
- Genomic analysis ofPeerJ · 2017Article
- Exploration of the Drosophila buzzatii transposable element content suggests underestimation of repeats in Drosophila genomes.BMC genomics · 2016Article
- Genomic signatures of domestication on neurogenetic genes in Drosophila melanogaster.BMC evolutionary biology · 2016Article
- Recombining without Hotspots: A Comprehensive Evolutionary Portrait of Recombination in Two Closely Related Species of Drosophila.Genome biology and evolution · 2015Article
- Article
- Background selection as baseline for nucleotide variation across the Drosophila genome.PLoS genetics · 2014Article
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Authors and funding
9 authors.
Funding
Abstract
Short-read sequencing techniques provide the opportunity to capture genome-wide sequence data in a single experiment. A current challenge is to identify questions that shallow-depth genomic data can address successfully and to develop corresponding analytical methods that are statistically sound. Here, we apply the Roche/454 platform to survey natural variation in strains of Drosophila melanogaster from an African (n = 3) and a North American (n = 6) population. Reads were aligned to the reference D. melanogaster genomic assembly, single nucleotide polymorphisms were identified, and nucleotide variation was quantified genome wide. Simulations and empirical results suggest that nucleotide diversity can be accurately estimated from sparse data with as little as 0.2x coverage per line. The unbiased genomic sampling provided by random short-read sequencing also allows insight into distributions of transposable elements and copy number polymorphisms found within populations and demonstrates that short-read sequencing methods provide an efficient means to quantify variation in genome organization and content. Continued development of methods for statistical inference of shallow-depth genome-wide sequencing data will allow such sparse, partial data sets to become the norm in the emerging field of population genomics.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.