Systematic generation of high-resolution deletion coverage of the Drosophila melanogaster genome.
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.
Parks
Annette L
AL
Exelixis, 170 Harbor Way, South San Francisco, California 94083-0511, USA.
Cook
Kevin R
KR
Belvin
Marcia
M
Dompe
Nicholas A
NA
Fawcett
Robert
R
Huppert
Kari
K
Tan
Lory R
LR
Winter
Christopher G
CG
Bogart
Kevin P
KP
Deal
Jennifer E
JE
Deal-Herr
Megan E
ME
Grant
Deanna
D
Marcinko
Marie
M
Miyazaki
Wesley Y
WY
Robertson
Stephanie
S
Shaw
Kenneth J
KJ
Tabios
Mariano
M
Vysotskaia
Valentina
V
Zhao
Lora
L
Andrade
Rachel S
RS
Edgar
Kyle A
KA
Howie
Elizabeth
E
Killpack
Keith
K
Milash
Brett
B
Norton
Amanda
A
Thao
Doua
D
Whittaker
Kellie
K
Winner
Millicent A
MA
Friedman
Lori
L
Margolis
Jonathan
J
Singer
Matthew A
MA
Kopczynski
Casey
C
Curtis
Daniel
D
Kaufman
Thomas C
TC
Plowman
Gregory D
GD
Duyk
Geoffrey
G
Francis-Lang
Helen L
HL
D000818:Animals; D004251:DNA Transposable Elements; D004331:Drosophila melanogaster / Q000235:genetics*; D016678:Genome; D016254:Mutagenesis, Insertional; D017384:Sequence Deletion
D004251:DNA Transposable Elements