title: Global diversity lines - a five-continent reference panel of sequenced Drosophila melanogaster strains.
abstract: Reference collections of multiple Drosophila lines with accumulating collections of "omics" data have proven especially valuable for the study of population genetics and complex trait genetics. Here we present a description of a resource collection of 84 strains of Drosophila melanogaster whose genome sequences were obtained after 12 generations of full-sib inbreeding. The initial rationale for this resource was to foster development of a systems biology platform for modeling metabolic regulation by the use of natural polymorphisms as perturbations. As reference lines, they are amenable to repeated phenotypic measurements, and already a large collection of metabolic traits have been assayed. Another key feature of these strains is their widespread geographic origin, coming from Beijing, Ithaca, Netherlands, Tasmania, and Zimbabwe. After obtaining 12.5× coverage of paired-end Illumina sequence reads, SNP and indel calls were made with the GATK platform. Thorough quality control was enabled by deep sequencing one line to >100×, and single-nucleotide polymorphisms and indels were validated using ddRAD-sequencing as an orthogonal platform. In addition, a series of preliminary population genetic tests were performed with these single-nucleotide polymorphism data for assessment of data quality. We found 83 segregating inversions among the lines, and as expected these were especially abundant in the African sample. We anticipate that this will make a useful addition to the set of reference D. melanogaster strains, thanks to its geographic structuring and unusually high level of genetic diversity.
authors: Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853.
authors: Jennifer K
authors: JK
authors: Grenier
authors: Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853 Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland CH-1015.
authors: J Roman
authors: JR
authors: Arguello
authors: Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853 Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland CH-1015.
authors: Margarida Cardoso
authors: MC
authors: Moreira
authors: Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853 Translational Medicine and Think Team, Otsuka Pharmaceutical Development and Commercialization, Inc., Princeton, New Jersey 08540.
authors: Srikanth
authors: S
authors: Gottipati
authors: Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, New York 14853.
authors: Jaaved
authors: J
authors: Mohammed
authors: Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853 Quantitative and Computational Biology, Princeton University, Princeton, New Jersey 08544.
authors: Sean R
authors: SR
authors: Hackett
authors: Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853.
authors: Rachel
authors: R
authors: Boughton
authors: Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853 Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, New York 14853.
authors: Anthony J
authors: AJ
authors: Greenberg
authors: Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853 Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, New York 14853 ac347@cornell.edu.
authors: Andrew G
authors: AG
authors: Clark
mesh_terms: D000483:Alleles; D000818:Animals; D016000:Cluster Analysis; D004331:Drosophila melanogaster / Q000235:genetics*; D005787:Gene Frequency; D014644:Genetic Variation; D005828:Genetics, Population; D016678:Genome; D005838:Genotype; D059014:High-Throughput Nucleotide Sequencing; D015810:Linkage Disequilibrium; D020641:Polymorphism, Single Nucleotide; D025341:Principal Component Analysis
keywords: D. melanogaster; global diversity lines; inversion polymorphism; residual heterozygosity; whole-genome sequences