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. 2004 Mar;36(3):288-92.
doi: 10.1038/ng1312. Epub 2004 Feb 22.

Systematic generation of high-resolution deletion coverage of the Drosophila melanogaster genome

Annette L Parks  1 , Kevin R Cook, Marcia Belvin, Nicholas A Dompe, Robert Fawcett, Kari Huppert, Lory R Tan, Christopher G Winter, Kevin P Bogart, Jennifer E Deal, Megan E Deal-Herr, Deanna Grant, Marie Marcinko, Wesley Y Miyazaki, Stephanie Robertson, Kenneth J Shaw, Mariano Tabios, Valentina Vysotskaia, Lora Zhao, Rachel S Andrade, Kyle A Edgar, Elizabeth Howie, Keith Killpack, Brett Milash, Amanda Norton, Doua Thao, Kellie Whittaker, Millicent A Winner, Lori Friedman, Jonathan Margolis, Matthew A Singer, Casey Kopczynski, Daniel Curtis, Thomas C Kaufman, Gregory D Plowman, Geoffrey Duyk, Helen L Francis-Lang
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Free article

Systematic generation of high-resolution deletion coverage of the Drosophila melanogaster genome

Annette L Parks et al. Nat Genet. 2004 Mar.
Free article

Abstract

In fruit fly research, chromosomal deletions are indispensable tools for mapping mutations, characterizing alleles and identifying interacting loci. Most widely used deletions were generated by irradiation or chemical mutagenesis. These methods are labor-intensive, generate random breakpoints and result in unwanted secondary mutations that can confound phenotypic analyses. Most of the existing deletions are large, have molecularly undefined endpoints and are maintained in genetically complex stocks. Furthermore, the existence of haplolethal or haplosterile loci makes the recovery of deletions of certain regions exceedingly difficult by traditional methods, resulting in gaps in coverage. Here we describe two methods that address these problems by providing for the systematic isolation of targeted deletions in the D. melanogaster genome. The first strategy used a P element-based technique to generate deletions that closely flank haploinsufficient genes and minimize undeleted regions. This deletion set has increased overall genomic coverage by 5-7%. The second strategy used FLP recombinase and the large array of FRT-bearing insertions described in the accompanying paper to generate 519 isogenic deletions with molecularly defined endpoints. This second deletion collection provides 56% genome coverage so far. The latter methodology enables the generation of small custom deletions with predictable endpoints throughout the genome and should make their isolation a simple and routine task.

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