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Natural variation in genome architecture among 205 Drosophila melanogaster Genetic Reference Panel lines.

  • Huang W Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina 27595, USA;
  • Massouras A Laboratory of Systems Biology and Genetics, Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland; Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland;
  • Inoue Y Center for Education in Liberal Arts and Sciences, Osaka University, Osaka-fu, 560-0043 Japan;
  • Peiffer J Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina 27595, USA;
  • Ràmia M Genomics, Bioinformatics and Evolution Group, Institut de Biotecnologia i de Biomedicina (IBB), Department of Genetics and Microbiology, Campus Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain;
  • Tarone AM Department of Entomology, Texas A&M University, College Station, Texas 77843, USA;
  • Turlapati L Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina 27595, USA;
  • Zichner T Genome Biology Unit, European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany;
  • Zhu D Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030 USA;
  • Lyman RF Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina 27595, USA;
  • Magwire MM Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina 27595, USA;
  • Blankenburg K Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030 USA;
  • Carbone MA Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina 27595, USA;
  • Chang K Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030 USA;
  • Ellis LL Department of Entomology, Texas A&M University, College Station, Texas 77843, USA;
  • Fernandez S Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030 USA;
  • Han Y Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030 USA;
  • Highnam G Virginia Tech Virginia Bioinformatics Institute and Department of Biological Sciences, Virginia Tech, Blacksburg, Virginia 24061, USA.
  • Hjelmen CE Department of Entomology, Texas A&M University, College Station, Texas 77843, USA;
  • Jack JR Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina 27595, USA;
  • Javaid M Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030 USA;
  • Jayaseelan J Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030 USA;
  • Kalra D Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030 USA;
  • Lee S Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030 USA;
  • Lewis L Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030 USA;
  • Munidasa M Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030 USA;
  • Ongeri F Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030 USA;
  • Patel S Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030 USA;
  • Perales L Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030 USA;
  • Perez A Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030 USA;
  • Pu L Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030 USA;
  • Rollmann SM Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina 27595, USA;
  • Ruth R Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030 USA;
  • Saada N Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030 USA;
  • Warner C Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030 USA;
  • Williams A Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030 USA;
  • Wu YQ Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030 USA;
  • Yamamoto A Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina 27595, USA;
  • Zhang Y Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030 USA;
  • Zhu Y Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030 USA;
  • Anholt RR Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina 27595, USA;
  • Korbel JO Genome Biology Unit, European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany;
  • Mittelman D Virginia Tech Virginia Bioinformatics Institute and Department of Biological Sciences, Virginia Tech, Blacksburg, Virginia 24061, USA.
  • Muzny DM Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030 USA;
  • Gibbs RA Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030 USA;
  • Barbadilla A Genomics, Bioinformatics and Evolution Group, Institut de Biotecnologia i de Biomedicina (IBB), Department of Genetics and Microbiology, Campus Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain;
  • Johnston JS Department of Entomology, Texas A&M University, College Station, Texas 77843, USA;
  • Stone EA Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina 27595, USA;
  • Richards S Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030 USA;
  • Deplancke B Laboratory of Systems Biology and Genetics, Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland; Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland;
  • Mackay TF Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina 27595, USA;
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  • 2014-04-10
Published in:
  • Genome research. - 2014
Animals
Chromatin
Drosophila melanogaster
Female
Genetic Linkage
Genetic Variation
Genome Size
Genome, Insect
Genome-Wide Association Study
Genotype
Genotyping Techniques
High-Throughput Nucleotide Sequencing
INDEL Mutation
Linkage Disequilibrium
Male
Molecular Sequence Annotation
Phenotype
Polymorphism, Single Nucleotide
Quantitative Trait, Heritable
Reproducibility of Results
English The Drosophila melanogaster Genetic Reference Panel (DGRP) is a community resource of 205 sequenced inbred lines, derived to improve our understanding of the effects of naturally occurring genetic variation on molecular and organismal phenotypes. We used an integrated genotyping strategy to identify 4,853,802 single nucleotide polymorphisms (SNPs) and 1,296,080 non-SNP variants. Our molecular population genomic analyses show higher deletion than insertion mutation rates and stronger purifying selection on deletions. Weaker selection on insertions than deletions is consistent with our observed distribution of genome size determined by flow cytometry, which is skewed toward larger genomes. Insertion/deletion and single nucleotide polymorphisms are positively correlated with each other and with local recombination, suggesting that their nonrandom distributions are due to hitchhiking and background selection. Our cytogenetic analysis identified 16 polymorphic inversions in the DGRP. Common inverted and standard karyotypes are genetically divergent and account for most of the variation in relatedness among the DGRP lines. Intriguingly, variation in genome size and many quantitative traits are significantly associated with inversions. Approximately 50% of the DGRP lines are infected with Wolbachia, and four lines have germline insertions of Wolbachia sequences, but effects of Wolbachia infection on quantitative traits are rarely significant. The DGRP complements ongoing efforts to functionally annotate the Drosophila genome. Indeed, 15% of all D. melanogaster genes segregate for potentially damaged proteins in the DGRP, and genome-wide analyses of quantitative traits identify novel candidate genes. The DGRP lines, sequence data, genotypes, quality scores, phenotypes, and analysis and visualization tools are publicly available.
Language
  • English
Open access status
hybrid
Identifiers
Persistent URL
https://sonar.ch/global/documents/180453
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