Natural variation in genome architecture among 205 Drosophila melanogaster Genetic Reference Panel lines
Huang, W. (North Carolina State University. Department of Biological Sciences)
Massouras, A. (Ecole Polytechnique Fédérale de Lausanne. Institute of Bioengineering)
Inoue, Y. (Osaka University. Center for Education in Liberal Arts and Sciences)
Peiffer, J. (North Carolina State University. Department of Biological Sciences)
Ràmia Jesús, Miquel (Universitat Autònoma de Barcelona. Institut de Biotecnologia i de Biomedicina "Vicent Villar Palasí")
Tarone, A. M. (Texas AandM University. Department of Entomology)
Turlapati, L. (North Carolina State University. Department of Biological Sciences)
Zichner, T. (European Molecular Biology Laboratory)
Zhu, Dianhui (Baylor College of Medicine. Human Genome Sequencing Center)
Lyman, R. F. (North Carolina State University. Department of Biological Sciences)
Magwire, M. M. (North Carolina State University. Department of Biological Sciences)
Blankenburg, K. (Baylor College of Medicine. Human Genome Sequencing Center)
Carbone, M. A. (North Carolina State University. Department of Biological Sciences)
Chang, K. (Baylor College of Medicine. Human Genome Sequencing Center)
Ellis, L. L. (Texas AandM University. Department of Entomology)
Fernandez, S. (Baylor College of Medicine. Human Genome Sequencing Center)
Han, Y. (Baylor College of Medicine. Human Genome Sequencing Center)
Highnam, G. (Virginia Tech. Virginia Bioinformatics Institute)
Hjelmen, C. E. (Texas AandM University. Department of Entomology)
Jack, J. R. (North Carolina State University. Department of Biological Sciences)
Javaid, M. (Baylor College of Medicine. Human Genome Sequencing Center)
Jayaseelan, J. C (Baylor College of Medicine. Human Genome Sequencing Center)
Kalra, D. (Baylor College of Medicine. Human Genome Sequencing Center)
Lee, S. (Baylor College of Medicine. Human Genome Sequencing Center)
Lewis, Lora (Baylor College of Medicine. Human Genome Sequencing Center)
Munidasa, M. (Baylor College of Medicine. Human Genome Sequencing Center)
Ongeri, F. (Baylor College of Medicine. Human Genome Sequencing Center)
Patel, Shohba (Baylor College of Medicine. Human Genome Sequencing Center)
Perales, L. (Baylor College of Medicine. Human Genome Sequencing Center)
Perez, Agapito (Baylor College of Medicine. Human Genome Sequencing Center)
Pu, L. L. (Baylor College of Medicine. Human Genome Sequencing Center)
Rollmann, S. M. (North Carolina State University. Department of Biological Sciences)
Ruth, R. (Baylor College of Medicine. Human Genome Sequencing Center)
Saada, N. (Baylor College of Medicine. Human Genome Sequencing Center)
Warner, C. (Shell International Exploration and Production, Inc.)
Williams, A. (Baylor College of Medicine. Human Genome Sequencing Center)
Wu, Y. Q. (Baylor College of Medicine. Human Genome Sequencing Center)
Yamamoto, A. (North Carolina State University. Department of Biological Sciences)
Zhang, Yiqing (Baylor College of Medicine. Human Genome Sequencing Center)
Zhu, Y. (Baylor College of Medicine. Human Genome Sequencing Center)
Anholt, Robert R. H (North Carolina State University. Department of Biological Sciences)
Korbel, Jan O. (European Molecular Biology Laboratory)
Mittelman, D. (Virginia Tech. Virginia Bioinformatics Institute. Department of Biological Sciences)
Muzny, D. M. (Baylor College of Medicine. Human Genome Sequencing Centere)
Gibbs, R. A. (Baylor College of Medicine. Human Genome Sequencing Center)
Barbadilla Prados, Antonio (Universitat Autònoma de Barcelona. Departament de Genètica i de Microbiologia)
Johnston, J. S. (Texas AandM University. Department of Entomology)
Stone, E. A. (North Carolina State University. Department of Biological Sciences)
Richards, S. (Baylor College of Medicine. Human Genome Sequencing Center)
Deplancke, Bart (Swiss Institute of Bioinformatics)
MacKay, T. F. C (North Carolina State University. Department of Biological Sciences)

Date:	2014
Abstract:	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.
Grants:	Ministerio de Ciencia e Innovación BFU2009-09504
Rights:	Aquest document està subjecte a una llicència d'ús Creative Commons. Es permet la reproducció total o parcial, la distribució, la comunicació pública de l'obra i la creació d'obres derivades, fins i tot amb finalitats comercials, sempre i quan es reconegui l'autoria de l'obra original.
Language:	Anglès
Document:	Article ; recerca ; Versió publicada
Subject:	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
Published in:	Genome research, Vol. 24, issue 7 (July 2014) , p. 1193-1208, ISSN 1549-5469

DOI: 10.1101/gr.171546.113
PMID: 24714809

16 p, 1.4 MB

The record appears in these collections:
Research literature > UAB research groups literature > Research Centres and Groups (research output) > Health sciences and biosciences > Institut de Biotecnologia i de Biomedicina (IBB)
Articles > Research articles
Articles > Published articles