The DrosDel Deletion Collection: A Drosophila Genomewide Chromosomal Deficiency Resource

Abstract

We describe a second-generation deficiency kit for Drosophila melanogaster composed of molecularly mapped deletions on an isogenic background, covering 77% of the Release 5.1 genome. Using a previously reported collection of FRT-bearing P-element insertions, we have generated 655 new deletions and verified a set of 209 deletion-bearing fly stocks. In addition to deletions, we demonstrate how the P elements may also be used to generate a set of custom inversions and duplications, particularly useful for balancing difficult regions of the genome carrying haplo-insufficient loci. We describe a simple computational resource that facilitates selection of appropriate elements for generating custom deletions. Finally, we provide a computational resource that facilitates selection of other mapped FRT-bearing elements that, when combined with the DrosDel collection, can theoretically generate over half a million precisely mapped deletions.T HE availability of chromosomal deletion collections is of considerable benefit to the Drosophila research community for gene mapping, the phenotypic characterization of alleles, and genomewide genetic interaction screens. A core deficiency kit, composed of 270 genetically heterogeneous deletions covering 92% of the genome, has been built up over many years by the Bloomington Drosophila Stock Center (BDSC; http:/ / flystocks.bio.indiana.edu/Browse/df-dp/dfkit-info.htm). Continuing efforts by the Bloomington Center are currently focused on expanding genome coverage by recovering deletions in the vicinity of haplo-insufficient regions (K. Cook, personal communication). Despite the considerable utility of this collection, it does, by its very nature, suffer from a number of limitations. These include a heterogeneous genetic background, the presence of uncharacterized second-site mutations, and, for most deletions, molecularly undefined breakpoints. More recently, two groups have taken advantage of two key technologies: large collections of transposon insertions precisely mapped to the Drosophila genome sequence and site-specific recombination, to develop tools for producing custom chromosomal deletions in homogeneous genetic backgrounds that are mapped to the genome sequence with single-base-pair resolution (Parks et al. 2004;Ryder et al. 2004;Thibault et al. 2004).Sequence data from this article have been deposited with the EMBL/ GenBank data libraries under accession nos. AJ545047-AJ547612 and AJ622065-AJ622812. In both cases, the new deletion collections are generated using FLP-mediated recombination between pairs of transposon-borne FRT sites, a method originally developed in Drosophila by Golic and Golic (1996). In one case (Parks et al. 2004), a set of .29,000 P-element and piggyBac insertions (Thibault et al. 2004) were used to generate 519 deletions covering 56% of the euchromatic genome (the Exelixis collection). The high number of starting insertions used by this group allows fine-scale coverage of the genome with relatively small deletions; the average size of the exist...

Methods to study Drosophila immunity

“…Transposon mutagenesis, albeit suffering from insertion bias [72], allows for easy retrieval of positional information, and forms the basis for a downstream toolkit of genetic applications including imprecise excision knock-out, Gal4-UAS overexpression of flanking genes, or element replacement by targeting vectors, to name but a few [73][74][75][76][77]. Extensive libraries of P-element-based transposon insertions are available through stock centers, along with deletion and duplication lines [78][79][80][81]. Finally, targeted gene knock-out using optimized targeting plasmids in combination with CRISPR will greatly accelerate full KO coverage of the fly genome [82].…”

Effect of genomic deficiencies on sexual size dimorphism through modification of developmental time in Drosophila melanogaster

“…These authors measured multiple phenotypic traits for a collection of DrosDel isogenic deficiency strains of D. melanogaster (Ryder et al, 2004) and the corresponding control strain. Because the breakpoints of the deletions in the deficiency strains were determined at a single base-pair resolution, they are a suitable tool for high resolution mapping of the candidate genomic regions (Ryder et al, 2004;Ryder et al, 2007). The control strain (DSK001: w 1118 iso ; 2 iso ; 3 iso ), whose X, second and third chromosomes are isogenized, share the same genetic background with the deficiency strains (Ryder et al, 2004;Ryder et al, 2007).…”

Toward a complete Drosophiladeficiency kit

“…Building on this, Golic and Golic [5] described how recombination between FRT sites carried on different chromosomes could be used to generate targeted chromosomal aberrations such as deletions and translocations. The principle behind the system is illustrated in Figure 1 and the FRT -bearing RS P elements developed for these elegant genome engineering approaches were used by the European DrosDel consortium to generate a collection of insertions for building a set of new deletions [6]. Using a conceptually similar approach, in this case with FRT sites carried on a set of piggyBac ( WH and RB ) and P ( XP ) transposon vectors, Exelixis Inc. also created a collection of new deletions [7].…”

“…In addition, each of the two collections was generated in a uniform genetic background and although these are different between the screens, it considerably reduces the genetic heterogeneity compared with the traditional collection. While neither of the new screens covered the entire genome (DrosDel covered 77% of the genome and Exelixis covered 56%), they did generate a combined total of around 20,000 FRT insertions across the fly genome with the potential to produce an estimated 500,000 precisely mapped FRT -derived deletions (FDDs) each of less than 1 Mb, covering 97% of the genome [6]. The utility of the new deletions and the underlying FRT insertions to the fly community is witnessed by over 500 citations to the publications describing them.…”

“…Minutes are generally associated with reduced dosage of genes encoding ribosomal proteins or core components of the translational machinery [10] and these regions represent a barrier to complete genome deficiency coverage since flies carrying deletions uncovering them are generally too sick to survive. While it is possible to recover deletions that include haploinsufficient loci by providing the fly with a covering duplication [6], such an approach has little utility in a deficiency kit since the duplication must always be present to rescue the insufficiency. Cook and colleagues chose to deal with this problem by generating deletions with breakpoints closely flanking each haploinsufficient locus, thus isolating it and providing close to full genome deletion coverage.…”