RT Journal
A1 Hoskins, Roger A.
A1 Carlson, Joseph W.
A1 Wan, Kenneth H.
A1 Park, Soo
A1 Mendez, Ivonne
A1 Galle, Samuel E.
A1 Booth, Benjamin W.
A1 Pfeiffer, Barret D.
A1 George, Reed A.
A1 Svirskas, Robert
A1 Krzywinski, Martin
A1 Schein, Jacqueline
A1 Accardo, Maria Carmela
A1 Damia, Elisabetta
A1 Messina, Giovanni
A1 Méndez-Lago, María
A1 de Pablos, Beatriz
A1 Demakova, Olga V.
A1 Andreyeva, Evgeniya N.
A1 Boldyreva, Lidiya V.
A1 Marra, Marco
A1 Carvalho, A. Bernardo
A1 Dimitri, Patrizio
A1 Villasante, Alfredo
A1 Zhimulev, Igor F.
A1 Rubin, Gerald M.
A1 Karpen, Gary H.
A1 Celniker, Susan E.
T1 The Release 6 reference sequence of the Drosophila melanogaster genome
JF Genome Research 
JO Genome Research 
YR 2015 
FD March 01 
VO 25 
IS 3 
SP 445 
OP 458 
DO 10.1101/gr.185579.114 
UL http://genome.cshlp.org/content/25/3/445.abstract 
AB 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.