@article {46499,
	title = {The Release 6 reference sequence of the Drosophila melanogaster genome.},
	journal = {Genome Research},
	volume = {25},
	year = {2015},
	month = {2015 Mar},
	pages = {445-58},
	abstract = {<p>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.</p>
},
	issn = {1549-5469},
	doi = {10.1101/gr.185579.114},
	author = {Hoskins, Roger A and Carlson, Joseph W and Wan, Kenneth H and Park, Soo and Mendez, Ivonne and Galle, Samuel E and Booth, Benjamin W and Pfeiffer, Barret D and George, Reed A and Svirskas, Robert and Krzywinski, Martin and Schein, Jacqueline and Accardo, Maria Carmela and Damia, Elisabetta and Messina, Giovanni and Mendez-Lago, Maria and de Pablos, Beatriz and Demakova, Olga V and Andreyeva, Evgeniya N and Boldyreva, Lidiya V and Marra, Marco and Carvalho, A Bernardo and Dimitri, Patrizio and Villasante, Alfredo and Zhimulev, Igor F and Rubin, Gerald M and Karpen, Gary H and Celniker, Susan E}
}
@article {988,
	title = {Tools for neuroanatomy and neurogenetics in Drosophila.},
	journal = {Proceedings of the National Academy of Sciences of the United States of America},
	volume = {105},
	year = {2008},
	month = {2008 Jul 15},
	pages = {9715-20},
	abstract = {<p>We demonstrate the feasibility of generating thousands of transgenic Drosophila melanogaster lines in which the expression of an exogenous gene is reproducibly directed to distinct small subsets of cells in the adult brain. We expect the expression patterns produced by the collection of 5,000 lines that we are currently generating to encompass all neurons in the brain in a variety of intersecting patterns. Overlapping 3-kb DNA fragments from the flanking noncoding and intronic regions of genes thought to have patterned expression in the adult brain were inserted into a defined genomic location by site-specific recombination. These fragments were then assayed for their ability to function as transcriptional enhancers in conjunction with a synthetic core promoter designed to work with a wide variety of enhancer types. An analysis of 44 fragments from four genes found that \&gt;80\% drive expression patterns in the brain; the observed patterns were, on average, comprised of \&lt;100 cells. Our results suggest that the D. melanogaster genome contains \&gt;50,000 enhancers and that multiple enhancers drive distinct subsets of expression of a gene in each tissue and developmental stage. We expect that these lines will be valuable tools for neuroanatomy as well as for the elucidation of neuronal circuits and information flow in the fly brain.</p>
},
	keywords = {Animals, Biomedical Research, Brain, Developmental, Drosophila melanogaster, Enhancer Elements, Gene Expression Regulation, Genes, Genetic, Genetically Modified, Insect, Neurons, Neurosciences, Recombination},
	issn = {1091-6490},
	doi = {https://doi.org/10.1073/pnas.0803697105},
	author = {Pfeiffer, Barret D and Jenett, Arnim and Hammonds, Ann S and Ngo, Teri-T B and Misra, Sima and Murphy, Christine and Scully, Audra and Carlson, Joseph W and Wan, Kenneth H and Laverty, Todd R and Mungall, Chris and Svirskas, Rob and Kadonaga, James T and Doe, Chris Q and Eisen, Michael B and Celniker, Susan E and Rubin, Gerald M}
}
