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Huang W, Massouras A, Inoue Y, Peiffer J, Ràmia M, Tarone AM, Turlapati L, Zichner T, Zhu D, Lyman RF, Magwire MM, Blankenburg K, Carbone MA, Chang K, Ellis LL, Fernandez S, Han Y, Highnam G, Hjelmen CE, Jack JR, Javaid M, Jayaseelan J, Kalra D, Lee S, Lewis L, Munidasa M, Ongeri F, Patel S, Perales L, Perez A, Pu L, Rollmann SM, Ruth R, Saada N, Warner C, Williams A, Wu YQ, Yamamoto A, Zhang Y, Zhu Y, Anholt RRH, Korbel JO, Mittelman D, Muzny DM, Gibbs RA, Barbadilla A, Johnston JS, Stone EA, Richards S, Deplancke B, Mackay TFC. Natural variation in genome architecture among 205 Drosophila melanogaster Genetic Reference Panel lines. Genome Res 2014; 24:1193-208. [PMID: 24714809 PMCID: PMC4079974 DOI: 10.1101/gr.171546.113] [Citation(s) in RCA: 415] [Impact Index Per Article: 41.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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.
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Affiliation(s)
- Wen Huang
- Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina 27595, USA
| | - Andreas Massouras
- 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
| | - Yutaka Inoue
- Center for Education in Liberal Arts and Sciences, Osaka University, Osaka-fu, 560-0043 Japan
| | - Jason Peiffer
- Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina 27595, USA
| | - Miquel Ràmia
- 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
| | - Aaron M Tarone
- Department of Entomology, Texas A&M University, College Station, Texas 77843, USA
| | - Lavanya Turlapati
- Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina 27595, USA
| | - Thomas Zichner
- Genome Biology Unit, European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany
| | - Dianhui Zhu
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030 USA
| | - Richard F Lyman
- Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina 27595, USA
| | - Michael M Magwire
- Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina 27595, USA
| | - Kerstin Blankenburg
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030 USA
| | - Mary Anna Carbone
- Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina 27595, USA
| | - Kyle Chang
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030 USA
| | - Lisa L Ellis
- Department of Entomology, Texas A&M University, College Station, Texas 77843, USA
| | - Sonia Fernandez
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030 USA
| | - Yi Han
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030 USA
| | - Gareth Highnam
- Virginia Tech Virginia Bioinformatics Institute and Department of Biological Sciences, Virginia Tech, Blacksburg, Virginia 24061, USA
| | - Carl E Hjelmen
- Department of Entomology, Texas A&M University, College Station, Texas 77843, USA
| | - John R Jack
- Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina 27595, USA
| | - Mehwish Javaid
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030 USA
| | - Joy Jayaseelan
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030 USA
| | - Divya Kalra
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030 USA
| | - Sandy Lee
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030 USA
| | - Lora Lewis
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030 USA
| | - Mala Munidasa
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030 USA
| | - Fiona Ongeri
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030 USA
| | - Shohba Patel
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030 USA
| | - Lora Perales
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030 USA
| | - Agapito Perez
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030 USA
| | - LingLing Pu
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030 USA
| | - Stephanie M Rollmann
- Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina 27595, USA
| | - Robert Ruth
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030 USA
| | - Nehad Saada
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030 USA
| | - Crystal Warner
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030 USA
| | - Aneisa Williams
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030 USA
| | - Yuan-Qing Wu
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030 USA
| | - Akihiko Yamamoto
- Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina 27595, USA
| | - Yiqing Zhang
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030 USA
| | - Yiming Zhu
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030 USA
| | - Robert R H Anholt
- Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina 27595, USA
| | - Jan O Korbel
- Genome Biology Unit, European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany
| | - David Mittelman
- Virginia Tech Virginia Bioinformatics Institute and Department of Biological Sciences, Virginia Tech, Blacksburg, Virginia 24061, USA
| | - Donna M Muzny
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030 USA
| | - Richard A Gibbs
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030 USA
| | - Antonio Barbadilla
- 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
| | - J Spencer Johnston
- Department of Entomology, Texas A&M University, College Station, Texas 77843, USA
| | - Eric A Stone
- Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina 27595, USA
| | - Stephen Richards
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030 USA
| | - Bart Deplancke
- 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
| | - Trudy F C Mackay
- Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina 27595, USA
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Rogers RL, Cridland JM, Shao L, Hu TT, Andolfatto P, Thornton KR. Landscape of standing variation for tandem duplications in Drosophila yakuba and Drosophila simulans. Mol Biol Evol 2014; 31:1750-66. [PMID: 24710518 PMCID: PMC4069613 DOI: 10.1093/molbev/msu124] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
We have used whole genome paired-end Illumina sequence data to identify tandem duplications in 20 isofemale lines of Drosophila yakuba and 20 isofemale lines of D. simulans and performed genome wide validation with PacBio long molecule sequencing. We identify 1,415 tandem duplications that are segregating in D. yakuba as well as 975 duplications in D. simulans, indicating greater variation in D. yakuba. Additionally, we observe high rates of secondary deletions at duplicated sites, with 8% of duplicated sites in D. simulans and 17% of sites in D. yakuba modified with deletions. These secondary deletions are consistent with the action of the large loop mismatch repair system acting to remove polymorphic tandem duplication, resulting in rapid dynamics of gain and loss in duplicated alleles and a richer substrate of genetic novelty than has been previously reported. Most duplications are present in only single strains, suggesting that deleterious impacts are common. Drosophila simulans shows larger numbers of whole gene duplications in comparison to larger proportions of gene fragments in D. yakuba. Drosophila simulans displays an excess of high-frequency variants on the X chromosome, consistent with adaptive evolution through duplications on the D. simulans X or demographic forces driving duplicates to high frequency. We identify 78 chimeric genes in D. yakuba and 38 chimeric genes in D. simulans, as well as 143 cases of recruited noncoding sequence in D. yakuba and 96 in D. simulans, in agreement with rates of chimeric gene origination in D. melanogaster. Together, these results suggest that tandem duplications often result in complex variation beyond whole gene duplications that offers a rich substrate of standing variation that is likely to contribute both to detrimental phenotypes and disease, as well as to adaptive evolutionary change.
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Affiliation(s)
- Rebekah L Rogers
- Department of Ecology and Evolutionary Biology, University of California, Irvine
| | - Julie M Cridland
- Department of Ecology and Evolutionary Biology, University of California, IrvineDepartment of Ecology and Evolutionary Biology, University of California, Davis
| | - Ling Shao
- Department of Ecology and Evolutionary Biology, University of California, Irvine
| | - Tina T Hu
- Department of Ecology and Evolutionary Biology and the Lewis Sigler Institute for Integrative Genomics, Princeton University
| | - Peter Andolfatto
- Department of Ecology and Evolutionary Biology and the Lewis Sigler Institute for Integrative Genomics, Princeton University
| | - Kevin R Thornton
- Department of Ecology and Evolutionary Biology, University of California, Irvine
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Sievers C, Comoglio F, Seimiya M, Merdes G, Paro R. A deterministic analysis of genome integrity during neoplastic growth in Drosophila. PLoS One 2014; 9:e87090. [PMID: 24516544 PMCID: PMC3916295 DOI: 10.1371/journal.pone.0087090] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2013] [Accepted: 12/19/2013] [Indexed: 11/18/2022] Open
Abstract
The development of cancer has been associated with the gradual acquisition of genetic alterations leading to a progressive increase in malignancy. In various cancer types this process is enabled and accelerated by genome instability. While genome sequencing-based analysis of tumor genomes becomes increasingly a standard procedure in human cancer research, the potential necessity of genome instability for tumorigenesis in Drosophila melanogaster has, to our knowledge, never been determined at DNA sequence level. Therefore, we induced formation of tumors by depletion of the Drosophila tumor suppressor Polyhomeotic and subjected them to genome sequencing. To achieve a highly resolved delineation of the genome structure we developed the Deterministic Structural Variation Detection (DSVD) algorithm, which identifies structural variations (SVs) with high accuracy and at single base resolution. The employment of long overlapping paired-end reads enables DSVD to perform a deterministic, i.e. fragment size distribution independent, identification of a large size spectrum of SVs. Application of DSVD and other algorithms to our sequencing data reveals substantial genetic variation with respect to the reference genome reflecting temporal separation of the reference and laboratory strains. The majority of SVs, constituted by small insertions/deletions, is potentially caused by erroneous replication or transposition of mobile elements. Nevertheless, the tumor did not depict a loss of genome integrity compared to the control. Altogether, our results demonstrate that genome stability is not affected inevitably during sustained tumor growth in Drosophila implying that tumorigenesis, in this model organism, can occur irrespective of genome instability and the accumulation of specific genetic alterations.
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Affiliation(s)
- Cem Sievers
- Department of Biosystems Science and Engineering, Swiss Federal Institute of Technology Zurich, Basel, Switzerland
| | - Federico Comoglio
- Department of Biosystems Science and Engineering, Swiss Federal Institute of Technology Zurich, Basel, Switzerland
| | - Makiko Seimiya
- Department of Biosystems Science and Engineering, Swiss Federal Institute of Technology Zurich, Basel, Switzerland
| | - Gunter Merdes
- Department of Biosystems Science and Engineering, Swiss Federal Institute of Technology Zurich, Basel, Switzerland
| | - Renato Paro
- Department of Biosystems Science and Engineering, Swiss Federal Institute of Technology Zurich, Basel, Switzerland ; Faculty of Science, University of Basel, Basel, Switzerland
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Erceg J, Saunders TE, Girardot C, Devos DP, Hufnagel L, Furlong EEM. Subtle changes in motif positioning cause tissue-specific effects on robustness of an enhancer's activity. PLoS Genet 2014; 10:e1004060. [PMID: 24391522 PMCID: PMC3879207 DOI: 10.1371/journal.pgen.1004060] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2013] [Accepted: 11/11/2013] [Indexed: 12/14/2022] Open
Abstract
Deciphering the specific contribution of individual motifs within cis-regulatory modules (CRMs) is crucial to understanding how gene expression is regulated and how this process is affected by sequence variation. But despite vast improvements in the ability to identify where transcription factors (TFs) bind throughout the genome, we are limited in our ability to relate information on motif occupancy to function from sequence alone. Here, we engineered 63 synthetic CRMs to systematically assess the relationship between variation in the content and spacing of motifs within CRMs to CRM activity during development using Drosophila transgenic embryos. In over half the cases, very simple elements containing only one or two types of TF binding motifs were capable of driving specific spatio-temporal patterns during development. Different motif organizations provide different degrees of robustness to enhancer activity, ranging from binary on-off responses to more subtle effects including embryo-to-embryo and within-embryo variation. By quantifying the effects of subtle changes in motif organization, we were able to model biophysical rules that explain CRM behavior and may contribute to the spatial positioning of CRM activity in vivo. For the same enhancer, the effects of small differences in motif positions varied in developmentally related tissues, suggesting that gene expression may be more susceptible to sequence variation in one tissue compared to another. This result has important implications for human eQTL studies in which many associated mutations are found in cis-regulatory regions, though the mechanism for how they affect tissue-specific gene expression is often not understood.
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Affiliation(s)
- Jelena Erceg
- Genome Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Timothy E. Saunders
- Genome Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Charles Girardot
- Genome Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Damien P. Devos
- Genome Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Lars Hufnagel
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Eileen E. M. Furlong
- Genome Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
- * E-mail:
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