title: The Release 6 reference sequence of the Drosophila melanogaster genome.
abstract: 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. Further significant improvements will require sequencing technologies that do not depend on molecular cloning and that produce very long reads.
authors.affiliation: Department of Genome Dynamics, Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA; RHoskins@lbl.gov celniker@fruitfly.org.
authors.forename: Roger A
authors.initials: RA
authors.lastname: Hoskins
authors.affiliation: Department of Genome Dynamics, Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA;
authors.forename: Joseph W
authors.initials: JW
authors.lastname: Carlson
authors.affiliation: Department of Genome Dynamics, Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA;
authors.forename: Kenneth H
authors.initials: KH
authors.lastname: Wan
authors.affiliation: Department of Genome Dynamics, Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA;
authors.forename: Soo
authors.initials: S
authors.lastname: Park
authors.affiliation: Department of Genome Dynamics, Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA;
authors.forename: Ivonne
authors.initials: I
authors.lastname: Mendez
authors.affiliation: Department of Genome Dynamics, Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA;
authors.forename: Samuel E
authors.initials: SE
authors.lastname: Galle
authors.affiliation: Department of Genome Dynamics, Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA;
authors.forename: Benjamin W
authors.initials: BW
authors.lastname: Booth
authors.affiliation: Janelia Farm Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia 20147, USA;
authors.forename: Barret D
authors.initials: BD
authors.lastname: Pfeiffer
authors.affiliation: Janelia Farm Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia 20147, USA;
authors.forename: Reed A
authors.initials: RA
authors.lastname: George
authors.affiliation: Janelia Farm Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia 20147, USA;
authors.forename: Robert
authors.initials: R
authors.lastname: Svirskas
authors.affiliation: Genome Sciences Centre, BC Cancer Agency, Vancouver, BC, V5Z 4S6, Canada;
authors.forename: Martin
authors.initials: M
authors.lastname: Krzywinski
authors.affiliation: Genome Sciences Centre, BC Cancer Agency, Vancouver, BC, V5Z 4S6, Canada;
authors.forename: Jacqueline
authors.initials: J
authors.lastname: Schein
authors.affiliation: Dipartimento di Biologia e Biotecnologie "Charles Darwin" and Istituto Pasteur Fondazione Cenci-Bolognetti, Sapienza Università di Roma, 00185 Roma, Italy;
authors.forename: Maria Carmela
authors.initials: MC
authors.lastname: Accardo
authors.affiliation: Dipartimento di Biologia e Biotecnologie "Charles Darwin" and Istituto Pasteur Fondazione Cenci-Bolognetti, Sapienza Università di Roma, 00185 Roma, Italy;
authors.forename: Elisabetta
authors.initials: E
authors.lastname: Damia
authors.affiliation: Dipartimento di Biologia e Biotecnologie "Charles Darwin" and Istituto Pasteur Fondazione Cenci-Bolognetti, Sapienza Università di Roma, 00185 Roma, Italy;
authors.forename: Giovanni
authors.initials: G
authors.lastname: Messina
authors.affiliation: Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Universidad Autónoma de Madrid, 28049 Madrid, Spain;
authors.forename: María
authors.initials: M
authors.lastname: Méndez-Lago
authors.affiliation: Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Universidad Autónoma de Madrid, 28049 Madrid, Spain;
authors.forename: Beatriz
authors.initials: B
authors.lastname: de Pablos
authors.affiliation: Institute of Molecular and Cellular Biology, Russian Academy of Sciences, Novosibirsk, 630090, Russia;
authors.forename: Olga V
authors.initials: OV
authors.lastname: Demakova
authors.affiliation: Institute of Molecular and Cellular Biology, Russian Academy of Sciences, Novosibirsk, 630090, Russia;
authors.forename: Evgeniya N
authors.initials: EN
authors.lastname: Andreyeva
authors.affiliation: Institute of Molecular and Cellular Biology, Russian Academy of Sciences, Novosibirsk, 630090, Russia;
authors.forename: Lidiya V
authors.initials: LV
authors.lastname: Boldyreva
authors.affiliation: Genome Sciences Centre, BC Cancer Agency, Vancouver, BC, V5Z 4S6, Canada;
authors.forename: Marco
authors.initials: M
authors.lastname: Marra
authors.affiliation: Departamento de Genética, Universidade Federal do Rio de Janeiro, CEP 21944-970, Rio de Janeiro, Brazil;
authors.forename: A Bernardo
authors.initials: AB
authors.lastname: Carvalho
authors.affiliation: Dipartimento di Biologia e Biotecnologie "Charles Darwin" and Istituto Pasteur Fondazione Cenci-Bolognetti, Sapienza Università di Roma, 00185 Roma, Italy;
authors.forename: Patrizio
authors.initials: P
authors.lastname: Dimitri
authors.affiliation: Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Universidad Autónoma de Madrid, 28049 Madrid, Spain;
authors.forename: Alfredo
authors.initials: A
authors.lastname: Villasante
authors.affiliation: Institute of Molecular and Cellular Biology, Russian Academy of Sciences, Novosibirsk, 630090, Russia; Novosibirsk State University, Novosibirsk, 630090, Russia;
authors.forename: Igor F
authors.initials: IF
authors.lastname: Zhimulev
authors.affiliation: Janelia Farm Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia 20147, USA;
authors.forename: Gerald M
authors.initials: GM
authors.lastname: Rubin
authors.affiliation: Department of Genome Dynamics, Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA; Department of Molecular and Cell Biology, University of California, Berkeley, California 94720, USA.
authors.forename: Gary H
authors.initials: GH
authors.lastname: Karpen
authors.affiliation: Department of Genome Dynamics, Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA; RHoskins@lbl.gov celniker@fruitfly.org.
authors.forename: Susan E
authors.initials: SE
authors.lastname: Celniker
mesh_terms: D000818:Animals; D002874:Chromosome Mapping; D022202:Chromosomes, Artificial, Bacterial; D019295:Computational Biology; D020451:Contig Mapping; D004331:Drosophila melanogaster / Q000235:genetics*; D016678:Genome; D059014:High-Throughput Nucleotide Sequencing; D017404:In Situ Hybridization, Fluorescence; D008969:Molecular Sequence Data; D059007:Polytene Chromosomes; D015183:Restriction Mapping