Genome

Drosophila melanogaster (fruit fly) This fruit fly has lead the way as a model organism in the study of genetics, development and disease Lineage: Eukaryota[15557]; Metazoa[7782]; Ecdysozoa[3517]; Arthropoda[3303]; Hexapoda[2975]; Insecta[2841]; Pterygota[2839]; Neoptera[2820]; Endopterygota[2630]; Diptera[678]; Brachycera[564]; Muscomorpha[552]; Ephydroidea[334]; Drosophilidae[331]; Drosophila[254]; Sophophora[111]; melanogaster group[80]; melanogaster subgroup[9]; Drosophila melanogaster[1]

From early observations of the banding patterns of its polytene chromosomes to current work on mRNA and protein gradients in the developing embryo, Drosophila melanogaster has been studied in biology labs for over eighty years. Many of the genes that define the spatial pattern of cell types and body parts have now been identified, along with More...the regulatory pathways in which they operate. As the majority of these genes have counterparts in higher eukaryotes, the study of the Drosophila developmental program provides insight into human development, as well.D. melanogaster is a member of the melanogaster group of the subgenus Sophophora and one of 12 fruit fly species whose genome is being sequenced to completion for use in comparative genomics studies. With previous information on the phylogenetic relationship between these species and the sequence of their genomes, a resource will be created that will provide reagents for studies in molecular evolution, gene function and comparative annotation across the entire Drosophila genus. Twenty fruit fly species have been approved for construction of BAC libraries, which will further assist in expanding our knowledge of gene homologies and pathway discovery. Less...

Summary Sequence data:  genome assemblies: 121; sequence reads: 77  (See  Genome Assembly and Annotation report) Statistics:  median total length (Mb): 136.463  median protein count: 30717  median GC%: 42.019 Publications (limited to 20 most recent records) Single-fly assemblies fill major phylogenomic gaps across the Drosophilidae Tree of Life. Kim BY, et al. bioRxiv 2023 Oct 2 Highly contiguous assemblies of 101 drosophilid genomes. Kim BY, et al. Elife 2021 Jul 19 A Transposon Story: From TE Content to TE Dynamic Invasion of Drosophila Genomes Using the Single-Molecule Sequencing Technology from Oxford Nanopore. Mohamed M, et al. Cells 2020 Jul 25 Adenine Methylation in Drosophila Is Associated with the Tissue-Specific Expression of Developmental and Regulatory Genes. Shah K, et al. G3 (Bethesda) 2019 Jun 5 The Release 6 reference sequence of the Drosophila melanogaster genome. Hoskins RA, et al. Genome Res 2015 Mar Numerous transitions of sex chromosomes in Diptera. Vicoso B, et al. PLoS Biol 2015 Apr Assembling large genomes with single-molecule sequencing and locality-sensitive hashing. Berlin K, et al. Nat Biotechnol 2015 Jun Gene Model Annotations for Drosophila melanogaster: The Rule-Benders. Crosby MA, et al. G3 (Bethesda) 2015 Jun 24 Gene Model Annotations for Drosophila melanogaster: Impact of High-Throughput Data. Matthews BB, et al. G3 (Bethesda) 2015 Jun 24 The Release 5.1 annotation of Drosophila melanogaster heterochromatin. Smith CD, et al. Science 2007 Jun 15 Sequence finishing and mapping of Drosophila melanogaster heterochromatin. Hoskins RA, et al. Science 2007 Jun 15 Combined evidence annotation of transposable elements in genome sequences. Quesneville H, et al. PLoS Comput Biol 2005 Jul Finishing a whole-genome shotgun: release 3 of the Drosophila melanogaster euchromatic genome sequence. Celniker SE, et al. Genome Biol 2002 Annotation of the Drosophila melanogaster euchromatic genome: a systematic review. Misra S, et al. Genome Biol 2002 The transposable elements of the Drosophila melanogaster euchromatin: a genomics perspective. Kaminker JS, et al. Genome Biol 2002 Heterochromatic sequences in a Drosophila whole-genome shotgun assembly. Hoskins RA, et al. Genome Biol 2002 The genome sequence of Drosophila melanogaster. Adams MD, et al. Science 2000 Mar 24 Drosophila melanogaster mitochondrial DNA: completion of the nucleotide sequence and evolutionary comparisons. Lewis DL, et al. Insect Mol Biol 1995 Nov Drosophila melanogaster mitochondrial DNA: gene organization and evolutionary considerations. Garesse R Genetics 1988 Apr Drosophila mitochondrial DNA: a novel gene order. Clary DO, et al. Nucleic Acids Res 1982 Nov 11 More...  Representative (genome information for reference and representative genomes) Reference genome:   Drosophila melanogaster Release 6 plus ISO1 MT Submitter: The FlyBase Consortium/Berkeley Drosophila Genome Project/Celera Genomics Loc Type Name RefSeq INSDC Size (Mb) GC% Protein rRNA tRNA Other RNA Gene Pseudogene Chr X NC_004354.4 AE014298.5 23.54 42.5 5,411 16 26 612 2,689 74 Chr 2L NT_033779.5 AE014134.6 23.51 41.8 5,707 - 41 973 3,515 52 Chr 2R NT_033778.4 AE013599.5 25.29 42.6 6,102 100 100 740 3,652 50 Chr 3L NT_037436.4 AE014296.5 28.11 41.7 5,906 - 50 811 3,486 41 Chr 4 NC_004353.4 AE014135.4 1.35 35.4 298 - - 40 114 7 Chr 3R NT_033777.3 AE014297.3 32.08 42.6 7,249 - 80 900 4,223 45 Chr Y NC_024512.1 CP007106.1 3.67 40.2 25 - - 28 113 62 MT NC_024511.2 KJ947872.2 0.02 17.8 13 2 22 - 37 - Un - . - 6.16 41.1 6 16 - 18 35 5 Chromosomes Click on chromosome name to open Genome Data Viewer External Resources BDGP FTP FlyBase OrthoDB UCSD Drosophila Species Stock Center FlyMine DFCI Drosophila Gene Index Trans-NIH Fly Initiative AAA - 12 Drosophila Genomes Drosophila Population Genomic Project UCSC Genome Browser Bloomington Drosophila Stock Center Vienna Drosophila RNAi Center Drosophila Genomics Resource Center CHORI BAC Libraries The Interactive Fly