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 approximately 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.

Figure 1.—

Structure of RS elements. (A) The orientation of RS3 and RS5 elements and their recombination products. 5′ and 3′ exons of the mini-white are marked by the open (RS3) or shaded (RS5) boxes. P-element ends are indicated by the triangles. FRT sites are designated by the solid arrows. (B) Recombination between an RS3r and an RS5r element in trans can generate a w⁺ deletion (I) or a w deletion (II), depending upon the relative orientations of the elements with respect to the chromosome. (C) Molecular strategies for confirming deletions (see materials and methods for details). The RS elements are as described in A. The locations of the primers described in materials and methods are shown as thin arrows with size of the PCR product indicated below each product.

Figure 2.—

Inversion types and the generation of aneuploid chromosomes. (A) Four types of inversion (right) are possible, depending upon the structure of the parental chromosome carrying the RS elements in cis (left). For clarity, we show the reduced forms of the elements (RSr). (B) Recombination between pairs of inversions produces aneuploid chromosomes. For illustration, we show the products of an exchange between a type 1 and a type 2 inversion, a w duplication (the parental line is w⁺) and a deletion carrying two copies of w⁺. Since the nonrecombinant progeny carry only a single copy of w⁺, the deletion may be identifiable by virtue of a darker eye color.

Figure 3.—

Map of the deletion coverage for chromosome arm 2L. The cytological map of 2L is given at the top and bottom, with the extent of each of the DrosDel deletions indicated. For clarity, the Df(2)ED prefix is omitted and only the deletion numbers are given.

Figure 4.—

Cytological verification of DrosDel deletions. Each deletion is heterozygous with a wild-type chromosome and the arrows indicate the location of the deletion. (A) Df(3R)ED6316 (99A5; 99C1, 527 kb). (B) Df(3L)ED4177 (61C2; 61E2, 715 kb). (C) Df(3L)ED4475 (68C13; 69B4, 821 kb).

Figure 5.—

Statistics of deletion recovery. (A) Deletion recovery frequency depends on the size of the deletion attempted. The percentage of deletion progeny recovered (Y axis) for deletions in a given size range (X axis), the bars represent standard deviations. (B) Absolute deletion recovery is affected by size, but not to a great extent. The frequency of success in generating deletions in the given size range is given, irrespective of the number of progeny that needed to be screened. (C) The extent of somatic mosaicism in heat-shocked flies carrying the RSr chromosomes in trans is a good indicator of successful deletion recovery. The frequency of deletion recovery (y-axis) for each of the indicated deletion size ranges is presented with respect to the subjective scoring of eye color mosaicism. In general parents with little mosaicism are less successful at producing deletion progeny.

Figure 6.—

Genome coverage of DrosDel and Exelixis deletions. For each chromosome arm, the coverage of DrosDel deletions that have been made is mapped to the Release 5.1 genome sequence. The coverage of extant Exelixis deletions mapped to the Release 3 sequence is given below. In many cases, gaps are complementary. The extent of coverage on the autosomes is similar for both collections; however, DrosDel has considerably better representation on the X and also covers approximately half of chromosome 4.

Figure 7.—

Duplication coverage for the distal half of 2L. A cytological map of the region of chromosome 2L from 21A1 to 32A4 with the location of the 41 duplications described in Table 4. Above the map, the locations of the lethal/haplo-insufficient regions rescued by the covering duplications described in Table 5 are indicated. Bar, 500 kb of genomic DNA.