FlyVar: a database for genetic variation in Drosophila melanogaster

FlyVar is a publicly and freely available platform that addresses the increasing need of next generation sequencing data analysis in the Drosophila research community. It is composed of three parts. First, a database that contains 5.94 million DNA polymorphisms found in Drosophila melanogaster derived from whole genome shotgun sequencing of 612 genomes of D. melanogaster. In addition, a list of 1094 dispensable genes has been identified. Second, a graphical user interface (GUI) has been implemented to allow easy and flexible queries of the database. Third, a set of interactive online tools enables filtering and annotation of genomic sequences obtained from individual D. melanogaster strains to identify candidate mutations. FlyVar permits the analysis of next generation sequencing data without the need of extensive computational training or resources. Database URL: www.iipl.fudan.edu.cn/FlyVar.

[1]  H. Harris.  Polymorphism and protein evolution. The neutral mutation-random drift hypothesis. , 1971, Journal of medical genetics.

[2]  M. W. Young,et al.  Nonessential Sequences, Genes, and the Polytene Chromosome Bands of DROSOPHILA MELANOGASTER. , 1978, Genetics.

[3]  H. Chandler.  Database , 1985 .

[4]  C. Aquadro,et al.  Levels of naturally occurring DNA polymorphism correlate with recombination rates in D. melanogaster , 1992, Nature.

[5]  M. C. Ellis,et al.  Single nucleotide polymorphism markers for genetic mapping in Drosophila melanogaster. , 2001, Genome research.

[6]  B. Dickson,et al.  Genetic mapping with SNP markers in Drosophila , 2001, Nature Genetics.

[7]  Sònia Casillas,et al.  DPDB: a database for the storage, representation and analysis of polymorphism in the Drosophila genus , 2005, ECCB/JBI.

[8]  C. Mungall,et al.  The Release 5.1 Annotation of Drosophila melanogaster Heterochromatin , 2007, Science.

[9]  D. Petrov,et al.  Evolution of gene function on the X chromosome versus the autosomes. , 2007, Genome dynamics.

[10]  B. Dickson,et al.  High-resolution, high-throughput SNP mapping in Drosophila melanogaster , 2008, Nature Methods.

[11]  J. Newberg,et al.  Identification of EMS-Induced Mutations in Drosophila melanogaster by Whole-Genome Sequencing , 2009, Genetics.

[12]  V. Hartenstein,et al.  Drosophila melanogaster , 2005 .

[13]  Takashi Suzuki,et al.  FLYSNPdb: a high-density SNP database of Drosophila melanogaster , 2009, Nucleic Acids Res..

[14]  H. Hakonarson,et al.  ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data , 2010, Nucleic acids research.

[15]  Raymond K. Auerbach,et al.  Integrative Analysis of the Caenorhabditis elegans Genome by the modENCODE Project , 2010, Science.

[16]  Bryan D. Kolaczkowski,et al.  Genomic Differentiation Between Temperate and Tropical Australian Populations of Drosophila melanogaster , 2011, Genetics.

[17]  K. Hughes,et al.  GENOMIC BASIS OF AGING AND LIFE‐HISTORY EVOLUTION IN DROSOPHILA MELANOGASTER , 2012, Evolution; international journal of organic evolution.

[18]  Colin N. Dewey,et al.  Genomic Variation in Natural Populations of Drosophila melanogaster , 2012, Genetics.

[19]  J. Mullikin,et al.  Analysis of DNA sequence variants detected by high‐throughput sequencing , 2012, Human mutation.

[20]  C. Schlötterer,et al.  Genome-wide patterns of latitudinal differentiation among populations of Drosophila melanogaster from North America , 2012, Molecular ecology.

[21]  Kenny Q. Ye,et al.  An integrated map of genetic variation from 1,092 human genomes , 2012, Nature.

[22]  Joseph K. Pickrell,et al.  A Systematic Survey of Loss-of-Function Variants in Human Protein-Coding Genes , 2012, Science.

[23]  Kevin R. Thornton,et al.  The Drosophila melanogaster Genetic Reference Panel , 2012, Nature.

[24]  Magalie S Leduc,et al.  Clinical whole-exome sequencing for the diagnosis of mendelian disorders. , 2013, The New England journal of medicine.

[25]  R. Gibbs,et al.  Natural variation in genome architecture among 205 Drosophila melanogaster Genetic Reference Panel lines. , 2014, Genome research.

[26]  Nele A. Haelterman,et al.  Large-scale identification of chemically induced mutations in Drosophila melanogaster , 2014, Genome research.

[27]  Jim Thurmond,et al.  FlyBase: introduction of the Drosophila melanogaster Release 6 reference genome assembly and large-scale migration of genome annotations , 2014, Nucleic Acids Res..