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Title: The Release 6 reference sequence of the Drosophila melanogaster genome

Journal Article · · Genome Research
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  1. Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
  2. Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Univ. of California, Berkeley, CA (United States)
  3. Howard Hughes Medical Inst., Ashburn, VA (United States). Janelia Farm Research Campus
  4. BC Cancer Agency, Vancouver, BC (Canada)
  5. Sapienza Univ. of Rome (Italy)
  6. Autonomous Univ. of Madrid (Spain)
  7. Russian Academy of Sciences (RAS), Moscow (Russian Federation)
  8. Federal Univ. of Rio de Janeiro (Brazil)
  9. Russian Academy of Sciences (RAS), Moscow (Russian Federation); Novosibirsk State Univ. (Russian Federation)

Drosophila melanogaster plays an important role in molecular, genetic, and genomic studies of heredity, development, metabolism, behavior, and human disease. The initial reference genome sequence reported more than a decade ago had a profound impact on progress in Drosophila research, and improving the accuracy and completeness of this sequence continues to be important to further progress. We previously described improvement of the 117-Mb sequence in the euchromatic portion of the genome and 21 Mb in the heterochromatic portion, using a whole-genome shotgun assembly, BAC physical mapping, and clone-based finishing. Here, we report an improved reference sequence of the single-copy and middle-repetitive regions of the genome, produced using cytogenetic mapping to mitotic and polytene chromosomes, clone-based finishing and BAC fingerprint verification, ordering of scaffolds by alignment to cDNA sequences, incorporation of other map and sequence data, and validation by whole-genome optical restriction mapping. These data substantially improve the accuracy and completeness of the reference sequence and the order and orientation of sequence scaffolds into chromosome arm assemblies. Representation of the Y chromosome and other heterochromatic regions is particularly improved. The new 143.9-Mb reference sequence, designated Release 6, effectively exhausts clone-based technologies for mapping and sequencing. Highly repeat-rich regions, including large satellite blocks and functional elements such as the ribosomal RNA genes and the centromeres, are largely inaccessible to current sequencing and assembly methods and remain poorly represented. In conclusion, further significant improvements will require sequencing technologies that do not depend on molecular cloning and that produce very long reads.

Research Organization:
Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)
Sponsoring Organization:
USDOE
Grant/Contract Number:
AC02- 05CH11231; AC0376SF00098; 13-04-40137; 12-04-00874-a; BFU2011-30295-C02-01; R01 GM064590
OSTI ID:
1257379
Journal Information:
Genome Research, Vol. 25, Issue 3; ISSN 1088-9051
Publisher:
Cold Spring Harbor Laboratory PressCopyright Statement
Country of Publication:
United States
Language:
English
Citation Metrics:
Cited by: 226 works
Citation information provided by
Web of Science

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Cited By (102)

FlyBase at 25: looking to the future journal October 2016
A fast‐evolving X‐linked duplicate of importin‐α2 is overexpressed in sex‐ratio drive in Drosophila neotestacea journal December 2018
Whole genome resequencing of a laboratory-adapted Drosophila melanogaster population sample journal January 2016
Pervasive epigenetic effects of Drosophila euchromatic transposable elements impact their evolution journal July 2017
Novel insights into endogenous RNA viral elements in Ixodes scapularis and other arbovirus vector genomes journal January 2019
Background selection as null hypothesis in population genomics: insights and challenges from Drosophila studies journal November 2017
Multi-faceted analysis provides little evidence for recurrent whole-genome duplications during hexapod evolution journal May 2020
Whole genome resequencing of a laboratory-adapted Drosophila melanogaster population sample journal January 2016
X-linkage is not a general inhibitor of tissue-specific gene expression in Drosophila melanogaster journal March 2017
Heterochromatin-enriched assemblies reveal the sequence and organization of the Drosophila melanogaster Y chromosome journal July 2018
Satellite DNA-containing gigantic introns in a unique gene expression program during Drosophila spermatogenesis journal May 2019
Independent origins of resistance or susceptibility of parasitic wasps to a defensive symbiont journal March 2016
A dual role of dLsd1 in oogenesis: regulating developmental genes and repressing transposons journal December 2019
Whole genome screen reveals a novel relationship between Wolbachia levels and Drosophila host translation journal July 2018
The Molecular and Genetic Characterization of Second Chromosome Balancers in Drosophila melanogaster journal February 2018
The Y chromosome contributes to sex-specific aging in Drosophila journal September 2019
Paternal Induction of Hybrid Dysgenesis in Drosophila melanogaster Is Weakly Correlated with Both P -Element and hobo Element Dosage journal March 2017
Adaptive evolution among cytoplasmic piRNA proteins leads to decreased genomic auto-immunity journal June 2020
SyRI: finding genomic rearrangements and local sequence differences from whole-genome assemblies journal December 2019
Characterization of Drosophila Nidogen / entactin reveals roles in basement membrane stability, barrier function and nervous system patterning journal December 2018
QTL mapping of natural variation reveals that the developmental regulator bruno reduces tolerance to P- element transposition in the Drosophila female germline journal June 2018
Dosage Compensation of X-Linked Muller Element F Genes but Not X-Linked Transgenes in the Australian Sheep Blowfly journal October 2015
Structural variants exhibit widespread allelic heterogeneity and shape variation in complex traits journal October 2019
Single-molecule sequencing resolves the detailed structure of complex satellite DNA loci in Drosophila melanogaster journal April 2017
Gene Regulatory Variation in Drosophila melanogaster Renal Tissue journal July 2018
Epigenetic analyses of planarian stem cells demonstrate conservation of bivalent histone modifications in animal stem cells journal August 2018
Direct interrogation of the role of H3K9 in metazoan heterochromatin function journal August 2016
Zinc Finger RNA-Binding Protein Zn72D Regulates ADAR-Mediated RNA Editing in Neurons journal May 2020
The structure of an endogenous Drosophila centromere reveals the prevalence of tandemly repeated sequences able to form i-motifs journal August 2015
A hybrid de novo genome assembly of the honeybee, Apis mellifera, with chromosome-length scaffolds journal April 2019
Stress response, behavior, and development are shaped by transposable element-induced mutations in Drosophila journal February 2019
Islands of retroelements are the major components of Drosophila centromeres journal February 2019
Hawaiian Drosophila genomes: size variation and evolutionary expansions journal January 2016
Birth of a new gene on the Y chromosome of Drosophila melanogaster journal September 2015
Establishment and evolution of heterochromatin journal February 2020
Efficient expression of genes in the Drosophila germline using a UAS-promoter free of interference by Hsp70 piRNAs journal March 2018
Fine-Scale Position Effects Shape the Distribution of Inversion Breakpoints in Drosophila melanogaster journal May 2020
Two modes of transvection at the eyes absent gene of Drosophila demonstrate plasticity in transcriptional regulatory interactions in cis and in trans journal May 2019
HITS-CLIP reveals sex-differential RNA binding and alterative splicing regulation of SRm160 in Drosophila journal May 2018
CRISPR Mutants of Three Y Chromosome Genes Suggest Gradual Evolution of Fertility Functions in Drosophila melanogaster journal January 2020
De novo assembly of a young Drosophila Y chromosome using single-molecule sequencing and chromatin conformation capture journal July 2018
Adaptive evolution among cytoplasmic piRNA proteins leads to decreased genomic auto-immunity journal January 2020
Zinc finger RNA binding protein Zn72D regulates ADAR-mediated RNA editing in neurons journal May 2019
Centromere-proximal meiotic crossovers in Drosophila melanogaster are suppressed by both highly-repetitive heterochromatin and the centromere effect journal May 2019
Arp2/3 and Unc45 maintain heterochromatin stability in Drosophila polytene chromosomes journal July 2019
Regulators of Long-Term Memory Revealed by Mushroom Body-Specific Gene Expression Profiling in Drosophila melanogaster journal June 2018
Rapid evolution of piRNA-mediated silencing of an invading transposable element was driven by abundant de novo mutations journal January 2020
A toolset to study functions of Cytosolic non-specific dipeptidase 2 (CNDP2) using Drosophila as a model organism journal March 2019
Heterochromatic hues of transcription—the diverse roles of noncoding transcripts from constitutive heterochromatin journal August 2019
Introgressive and horizontal acquisition of Wolbachia by Drosophila yakuba -clade hosts and horizontal transfer of incompatibility loci between distantly related Wolbachia journal August 2019
flyDIVaS : A Comparative Genomics Resource for Drosophila Divergence and Selection journal May 2016
Fine-scale position effects shape the distribution of inversion breakpoints in Drosophila melanogaster journal October 2019
Canu: scalable and accurate long-read assembly via adaptive k -mer weighting and repeat separation journal March 2017
RNA from a simple-tandem repeat is required for sperm maturation and male fertility in Drosophila melanogaster journal November 2019
New slbo-Gal4 driver lines for the analysis of border cell migration during Drosophila oogenesis journal July 2018
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FlyBase at 25: looking to the future. text January 2017
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Scrutinizing the immune defence inventory of Camponotus floridanus applying total transcriptome sequencing journal July 2015
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Single molecule long read sequencing resolves the detailed structure of complex satellite DNA loci in Drosophila melanogaster journal July 2016
Whole genome screen reveals a novel relationship between Wolbachia levels and Drosophila host translation journal November 2018
Gene Model Annotations for Drosophila melanogaster : Impact of High-Throughput Data journal June 2015
Nuclear F-actin and myosins drive relocalization of heterochromatic breaks journal June 2018
Genetic and Molecular Analysis of Essential Genes in Centromeric Heterochromatin of the Left Arm of Chromosome 3 in Drosophila melanogaster journal April 2019
Re-annotation of eight Drosophila genomes journal December 2018
GENOME REPORT: High-quality genome assemblies of 15 Drosophila species generated using Nanopore sequencing journal June 2018
Satellite DNA-containing gigantic introns in a unique gene expression program during Drosophila spermatogenesis journal December 2018
Comparative Analysis of Satellite DNA in the Drosophila melanogaster Species Complex journal December 2016
De novo assembly of a young Drosophila Y chromosome using Single-Molecule sequencing and Chromatin Conformation capture journal May 2018
Host–transposon interactions: conflict, cooperation, and cooption journal September 2019
Epigenetic analyses of planarian stem cells demonstrate conservation of bivalent histone modifications in animal stem cells journal August 2018
And yet, it moves: nuclear and chromatin dynamics of a heterochromatic double-strand break
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  • Philosophical Transactions of the Royal Society B: Biological Sciences, Vol. 372, Issue 1731 https://doi.org/10.1098/rstb.2016.0291
journal August 2017
SEX-DETector: A Probabilistic Approach to Study Sex Chromosomes in Non-Model Organisms text January 2016
SEX-DETector: A Probabilistic Approach to Study Sex Chromosomes in Non-Model Organisms journal August 2016
QTL mapping of natural variation reveals that the developmental regulator bruno reduces tolerance to P-element transposition in the Drosophila female germline journal October 2018
Efficient Expression of Genes in the Drosophila Germline Using a UAS Promoter Free of Interference by Hsp70 piRNAs journal April 2018
Heterochromatin-Enriched Assemblies Reveal the Sequence and Organization of the Drosophila melanogaster Y Chromosome journal November 2018
DNA sequence models of genome-wide Drosophila melanogaster Polycomb binding sites improve generalization to independent Polycomb Response Elements journal July 2019
On the Importance to Acknowledge Transposable Elements in Epigenomic Analyses journal March 2019
Arp2/3 and Unc45 maintain heterochromatin stability in Drosophila polytene chromosomes journal June 2019
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Heterochromatic breaks move to the nuclear periphery to continue recombinational repair journal October 2015
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Direct interrogation of the role of H3K9 in metazoan heterochromatin function text January 2016
Amphioxus SYCP1: a case of retrogene replacement and co-option of regulatory elements adjacent to the ParaHox cluster journal January 2018
The absence of crossovers on chromosome4inDrosophila melanogaster: Imperfection or interesting exception? journal May 2017
Cervantes and Quijote protect heterochromatin from aberrant recombination and lead the way to the nuclear periphery journal September 2016
Invasion of the P elements: Tolerance is not futile journal October 2018
Islands of retroelements are major components of Drosophila centromeres journal May 2019
Taming the giant within journal May 2019
Identification of Bari Transposons in 23 Sequenced Drosophila Genomes Reveals Novel Structural Variants, MITEs and Horizontal Transfer journal May 2016
Whole Genome Mapping with Feature Sets from High-Throughput Sequencing Data journal September 2016
Adenine Methylation in Drosophila Is Associated with the Tissue-Specific Expression of Developmental and Regulatory Genes journal June 2019
An Interscholastic Network To Generate LexA Enhancer Trap Lines inDrosophila journal July 2019
A Drosophila model of cigarette smoke induced COPD identifies Nrf2 signaling as an expedient target for intervention journal August 2018
Drosophila As a Genetically Tractable Model for Social Insect Behavior journal April 2016
H3K9 Promotes Under-Replication of Pericentromeric Heterochromatin in Drosophila Salivary Gland Polytene Chromosomes journal January 2019

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