Phenotypes Associated with Second Chromosome P Element Insertions in Drosophila melanogaster

Lily Kahsai; Gillian H Millburn; Kevin R Cook

doi:10.1534/g3.116.030940

. 2016 Jun 10;6(8):2665–2670. doi: 10.1534/g3.116.030940

Phenotypes Associated with Second Chromosome P Element Insertions in Drosophila melanogaster

Lily Kahsai ^*, Gillian H Millburn ^†, Kevin R Cook ^*,¹

PMCID: PMC4978919 PMID: 27317776

Abstract

In Drosophila melanogaster, P element transposition has been a productive means of insertional mutagenesis. Thousands of genes have been tagged with natural and engineered P element constructs. Nevertheless, chromosomes carrying P element insertions tend to have high levels of background mutations from P elements inserting and excising during transposition. Consequently, the phenotypes seen when P element-bearing chromosomes are homozygous are often not attributable to the P insertions themselves. In this study, 178 strains in the Bloomington Drosophila Stock Center collection with P insertions on the second chromosome were complementation tested against molecularly defined chromosomal deletions and previously characterized single-gene mutations to determine if recessive lethality or sterility is associated with the P insertions rather than background mutations. This information should prove valuable to geneticists using these strains for experimental studies of gene function.

Keywords: Drosophila melanogaster, P element, insertional mutagenesis, complementation, phenotypic characterization

During P element transposition, it is common for a P element to insert into a chromosome and immediately excise, leaving a mutational footprint, before inserting into the genome in its final position (Cooley et al. 1988, Kania et al. 1995, Deak et al. 1997, Salzberg et al. 1997, Spradling et al. 1999, Ashburner et al. 2005). These “hit and run” events often disrupt genes; consequently, the phenotypes seen when insertion-bearing chromosomes are made homozygous cannot necessarily be attributed to the disruption of genes where P elements are located. Proof that a phenotype is associated with a P element insertion usually comes from reverting the phenotype upon transposase-mediated excision of the P element or showing that the P insertion fails to complement a loss-of-function mutation in the gene where the P insertion is found.

Most P element insertions from early Drosophila transposition screens were given symbols that reflected the phenotypes seen when the chromosomes were made homozygous (Spradling et al. 1999). For example, P{lacW}l(2)k01209^k01209 was named as a recessive lethal on the second chromosome [“l(2)”], while other insertions were named for phenotypes such as female sterility (fs) and male sterility (ms). The Berkeley Drosophila Genome Project put considerable effort into verifying the phenotypes of P insertions by complementation testing the insertions against chromosomal deletions, other P insertions, and previously characterized loss-of-function mutations (Spradling et al. 1999). In addition, many labs have investigated the phenotypes of particular insertions. Nevertheless, the purported phenotypes of hundreds of P insertions from early screens have never been confirmed, and insertions from more recent screens have generally been given phenotype-neutral symbols. In the study described here, we analyzed 178 second chromosome P insertions with potentially misleading symbols in the Bloomington Drosophila Stock Center collection to determine whether the insertions are responsible for recessive lethal or sterile phenotypes.

Materials and Methods

Our approach was straightforward: we identified chromosomal deletions that encompass the insertion sites of P elements, made complementation crosses between deletion and P insertion stocks, and scored the appropriate progeny classes for lethality, female sterility, or male sterility. Assessing P insertions that had previously been localized to a specific genomic sequence often required only a single deletion cross. P elements that had previously been localized by in situ hybridization of polytene chromosome preparations were tested with a tiling series of deletions that spanned the genomic regions estimated to contain the insertions. Occasionally, single-gene mutations were complementation tested against the P insertions instead of deletions, or in addition to deletions. As positive controls, all deletion and single-gene mutation stocks were complementation tested against relevant, previously characterized, loss-of-function mutations (Supplemental Material, Table S1). All stocks were obtained from the Bloomington Drosophila Stock Center collection. All crosses were made on standard medium and reared under routine conditions. All genomic coordinates are given in terms of the Release 6 assembly. Polytene cytologies were estimated from Release 6 coordinates using FlyBase map conversion tables. Genetic symbols were changed to reflect our findings according to standard FlyBase nomenclatural practices.

Data availability

Changes to FlyBase entries have been coordinated with this report and will appear in a 2016 FlyBase update. Strains may be obtained from the Bloomington Drosophila Stock Center.

Results and Discussion

Table 1 shows the results of complementation tests with 95 P element stocks that indicate the recessive phenotypes seen when insertion chromosomes are made homozygous do not map to the P insertions themselves. Based on these results, we updated most of the insertion symbols. If the P insertion was positioned between genes, then the symbol was updated to show it as a simple insertion implying nothing about phenotypes. For example, P{PZ}l(2)10333¹⁰³³³ was changed to P{PZ}10333. We updated 38 symbols in this way. If the P element insertion was positioned within the transcribed portion of an annotated gene, the symbol was updated to show the insertion as an allele of the gene, but the updated FlyBase entry indicates that no known phenotype is associated with the insertion. For example, P{lacW}l(2)k09610^k09610 was changed to P{lacW}ush^k09610. We updated 47 symbols in this way. Since the lethality or sterility of these insertion chromosomes does not map to the insertion, and there is no way to know if it is the result of a single mutation or multiple mutations without further tests, the original gene and allele entries have been eliminated from FlyBase. For example, the l(2)10333 and l(2)k09610 gene entries, and the l(2)10333¹⁰³³³ and l(2)k09610^k09610 allele entries have been eliminated. The gene and allele entries for noninsertion mutations were retained only when the phenotypes of the mutations have been characterized beyond simple lethality or sterility, or when the mutations are members of multiallele complementation groups. For example, P{lacW}bdg^k08407 now represents the site of a nonlethal P insertion, and l(2)k08407^k08407 represents the linked noninsertion lethal mutation formerly conflated under P{lacW}l(2)k08407^k08407. In this case, it is necessary to have an allele entry for the noninsertion l(2)k08407^k08407 mutation because there is presumably a single mutation causing the imaginal disc abnormalities described in Roch et al. (1998) for the homozygous chromosome.

Table 1. Insertions with no associated lethal or sterile phenotype.

Original Symbol	Previous Mapping^a	Complementing Deletions and Mutations	Phenotype^b	New Insertion Symbol	New Allele^c
P{f⁺13}l(2)37Co¹	in situ	Df(2L)BSC341	v	P{f⁺13}37C
P{lacW}rack^k15001	seq	Df(2R)BSC160, Df(2R)ED2247	v	P{lacW}tou^k15001
P{hsneo}fs(2)neo9¹	in situ	Df(2L)C144	ff	P{hsneo}neo9
P{hsneo}fs(2)neo12¹	in situ	Df(2R)ED2247	ff	P{hsneo}neo12
P{Cp38::Adh}mfs(2)1¹	in situ	Df(2L)ED1473, Df(2L)ED1378	mf, ff	P{Cp38::Adh}1
P{lacW}l(2)k01301^k01301	seq	Df(2R)FDD-0003576	v	P{lacW}CR43651^k01301
P{lacW}l(2)k01302^k01302	seq	Df(2L)BSC693	v	P{lacW}tkv^k01302	CR14033^k01302
P{lacW}l(2)k02205^k02205	seq	Df(2R)BSC482	v	P{lacW}sli^k02205
P{lacW}l(2)k02520^k02520	seq	Df(2R)Exel6050	v	P{lacW}k02520
P{lacW}l(2)k03110^k03110	seq	Df(2R)ED3181	v, h	P{lacW}k03110
P{lacW}l(2)k03111^k03111	seq	Df(2R)BSC131	v	P{lacW}CG1648^k03111
P{lacW}l(2)k03204^k03204	seq	Df(2R)BSC326	v	P{lacW}jing^k03204
P{lacW}l(2)k03609^k03609	seq	Df(2R)Exel7142	v	P{lacW}k03609
P{lacW}l(2)k05420^k05420	seq	Df(2R)BSC131	v	P{lacW}k05420
P{lacW}l(2)k05421^k05421	seq	Df(2R)ED3181	v, h	P{lacW}CG6426^k05421
P{lacW}l(2)k05812^k05812	seq	Df(2L)BSC145	ff	P{lacW}piwi^k05812
P{lacW}l(2)k06402^k06402	seq	Df(2R)BSC154	v	P{lacW}k06402
P{lacW}l(2)k06904^k06904	seq	Df(2R)Exel7173, Df(2R)ED3952	v	P{lacW}k06904
P{lacW}l(2)k07005^k07005	seq	Df(2L)BSC107	v	P{lacW}k07005
P{lacW}l(2)k07015^k07015	seq	Df(2L)BSC855	v	P{lacW}k07015
P{lacW}Sema-2b^k07127	seq	Df(2R)Exel7142	v
P{lacW}l(2)k07237^k07237	seq	Df(2R)BSC133	v	P{lacW}k07237
P{lacW}k07406	seq	Df(2R)ED3385	v	P{lacW}CG14480^k07406
P{lacW}l(2)k07509^k07509	seq		h	P{lacW}k07509
P{lacW}l(2)k07914^k07914	seq	Df(2L)BSC340, Df(2L)BSC159	v	P{lacW}k07914
P{lacW}l(2)k08002^k08002	seq	18w^Delta7-35, 18w^k02701	v	P{lacW}k08002
P{lacW}l(2)k08407^k08407	seq	Df(2R)BSC482, Df(2R)Exel7138	v	P{lacW}bdg^k08407
P{lacW}l(2)k08504^k08504	seq	Df(2R)ED1735, Df(2R)Exel6055	v	P{lacW}ACC^k08504	Nup44A^k08504
P{lacW}l(2)k08816^k08816	seq	Df(2R)BSC133	v	P{lacW}CG12744^k08816
P{lacW}l(2)k08915^k08915	seq	Df(2L)BSC107	v	P{lacW}cbt^k08915	ush^k08915
P{lacW}l(2)k09202^k09202	seq	Df(2R)Exel6066	v, h	P{lacW}k09202
P{lacW}l(2)k09221^k09221	seq	Df(2R)BSC132	v	P{lacW}k09221
P{lacW}l(2)k09610^k09610	seq	Df(2L)BSC107	v	P{lacW}ush^k09610
P{lacW}l(2)k09854^k09854	seq	Df(2R)BSC433	v	P{lacW}GstS1^k09854
P{lacW}l(2)k09920^k09920	seq	Df(2R)Exel6070, Df(2R)BSC430	v	P{lacW}k09920
P{lacW}l(2)k09923^k09923	seq	Df(2L)ED369, Df(2L)BSC185	v	P{lacW}k09923
P{lacW}l(2)k09924^k09924	seq	Df(2R)BSC347	v	P{lacW}k09924
P{lacW}l(2)k10003a^k10003a	seq	Df(2L)Exel8013	v	P{lacW}k10003a
P{lacW}l(2)k10004^k10004	seq	Df(2L)Exel9062	v	P{lacW}k10004
P{lacW}l(2)k10113^k10113	seq	Df(2L)ED479	v	P{lacW}k10113
P{lacW}l(2)k10127^k10127	seq	Df(2L)BSC172	v	P{lacW}Tfb5^k10127	CG31917^k10127
P{lacW}l(2)k10217^k10217	seq	Df(2L)ED7853	v	P{lacW}CR45716^k10217
P{lacW}l(2)k10609^k10609	seq	Df(2L)ED479	v	P{lacW}RapGAP1^k10609
P{lacW}l(2)k10815^k10815	seq	Df(2R)BSC433	v, h	P{lacW}GstS1^k10815
P{lacW}l(2)k11120a^k11120a	seq	Df(2R)BSC408	v	P{lacW}k11120a
P{lacW}l(2)k11206^k11206	seq	Df(2L)BSC109	v	P{lacW}pgant5^k11206
P{lacW}l(2)k11301^k11301	seq	Df(2R)BSC433	v	P{lacW}GstS1^k11301
P{lacW}l(2)k11311^k11311	seq	Df(2R)BSC347	v	P{lacW}k11311
P{lacW}l(2)k11404^k11404	seq	Df(2R)BSC463	v	P{lacW}CG34021^k11404
P{lacW}l(2)k11405^k11405	seq	Df(2R)BSC433	v	P{lacW}GstS1^k11405
P{lacW}l(2)k13211^k13211	seq	Df(2R)ED3952	v	P{lacW}k13211
P{lacW}l(2)k13617^k13617	seq	Df(2R)ED2751	v	P{lacW}Dek^k13617
P{lacW}l(2)k14206^k14206	seq	Df(2L)BSC187	v	P{lacW}Tango1^k14206
P{lacW}l(2)k15617^k15617	seq	Df(2R)ED2457	v	P{lacW}Dg^k15617
P{lacW}l(2)k16215^k16215	seq	Df(2L)Exel7066	v, h	P{lacW}CG5953^k16215
P{lacW}l(2)k16406^k16406	seq	Df(2L)BSC101, tsh⁸	v	P{lacW}k16406
P{lacW}l(2)k16919^k16919	seq	Df(2L)Exel7034	v	P{lacW}Bsg^k16919
P{PZ}l(2)03050⁰³⁰⁵⁰	seq	Df(2R)Exel6071	v	P{PZ}ND-B14.7⁰³⁰⁵⁰
P{PZ}l(2)03497⁰³⁴⁹⁷	seq	Df(2R)BSC280, Df(2R)BSC408	v	P{PZ}wun⁰³⁴⁹⁷
P{PZ}l(2)03605⁰³⁶⁰⁵	seq		h	P{PZ}Tango1¹⁰³⁶⁰⁵
P{PZ}emm¹	seq	Df(2R)BSC594, Df(2R)BSC883	mf	P{PZ}06268
P{PZ}l(2)rL220^rL220	seq	Df(2L)BSC142	v	P{PZ}cdc14^rL220
P{lacW}l(2)s2978^s2978	seq	Df(2L)ED678, Df(2L)BSC203	v	P{lacW}rost^s2978
P{PZ}l(2)rK639^rK639	seq	Df(2L)BSC290	v	P{PZ}rK639
P{lacW}l(2)s1878^s1878	seq	Df(2R)Exel7162, PCNA²⁷³⁵, PCNA^k00704, PCNA⁰²⁴⁴⁸	ff	P{lacW}PCNA^s1878
P{PZ}l(2)rAO135^rAO135	seq	Df(2L)BSC102, tsh⁸	v	P{PZ}tsh^rAO135
P{lacW}l(2)k02107a^k02107a	in situ	Df(2R)ED1742, Df(2R)BSC269	v	P{lacW}k02107a
P{lacW}fs(2)k09833^k09833	in situ	Df(2R)Exel7121	ff	P{lacW}k09833
P{lacW}l(2)k07136^k07136	seq	Df(2R)BSC698	v	P{lacW}k07136
P{lacW}l(2)s4830^s4830	seq	Df(2R)BSC661	v	P{lacW}CG43795^s4830
P{lacW}l(2)k00808^k00808	seq	Df(2R)BSC603	v	P{lacW}mAChR-A^k00808
P{lacW}l(2)k03205^k03205	seq	Df(2R)BSC607	v	P{lacW}NKAIN^k03205	CR43466^k03205
P{PZ}l(2)07806⁰⁷⁸⁰⁶	seq	Df(2R)BSC814	v	P{PZ}CG34115⁰⁷⁸⁰⁶
P{PZ}l(2)07837⁰⁷⁸³⁷	seq	Df(2R)BSC802	v	P{PZ}Fili⁰⁷⁸³⁷
P{PZ}l(2)10491¹⁰⁴⁹¹	seq	Df(2R)BSC154	v	P{PZ}cnk¹⁰⁴⁹¹
P{PZ}l(2)10505¹⁰⁵⁰⁵	seq	Df(2R)ED3385	v	P{PZ}CG30105¹⁰⁵⁰⁵
P{PZ}l(2)10333¹⁰³³³	seq	Df(2L)Exel6034	v	P{PZ}10333
P{Mae-UAS.6.11}LA00508^LA00508	seq	Df(2L)ED611	v	P{Mae-UAS.6.11}LA00508
P{lacW}l(2)SH0108^SH0108	seq	Df(2R)BSC274	ff	P{lacW}mip120^SH0108
P{lacW}bchs^SH0148	seq	Df(2L)Exel7024	v, h
P{lacW}l(2)SH0237^SH0237	seq	Df(2R)BSC274	v	P{lacW}SH0237
P{lacW}l(2)SH0294^SH0294	seq	Df(2R)BSC597	v	P{lacW}wdp^SH0294
P{lacW}Phax^SH0641	seq		h
P{lacW}Galphas^SH0782	seq	Df(2R)BSC601	v
P{lacW}ItgaPS5^SH1114	seq	Df(2R)BSC785	v
P{lacW}CG4266^SH1128	seq	Df(2R)BSC484	v
P{lacW}l(2)SH1372^SH1372	seq	Df(2L)ED343	v, h	P{lacW}Tsp26A^SH1372
P{lacW}l(2)SH1393^SH1393	seq		h	P{lacW}Prosalpha7^SH1393
P{lacW}CG30015^SH1405	seq	Df(2R)ED2098, Df(2R)BSC327	v, h
P{lacW}mbm^SH1819	seq	Df(2L)ED19	v
P{lacW}Snp^SH1834	seq		h
P{lacW}l(2)SH1927^SH1927	seq	Df(2R)BSC153, Df(2R)BSC259	v	P{lacW}SH1927
P{lacW}hebe^SH2065	seq	Df(2R)BSC131	v, h
P{lacW}l(2)SH2138^SH2138	seq	Df(2R)BSC770	v	P{lacW}SH2138
P{lacW}oho48A^k06524	seq	Df(2R)ED2247, Df(2R)ED2219	v	P{lacW}CG9005^k06524

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In situ, insertion mapped by in situ hybridization to polytene chromosomes; seq, insertion mapped from sequence of insertion site.

Phenotype in complementation tests: v, viable; ff, female fertile; mf, male fertile. An “h” indicates homozygotes were present in stocks (in some of these cases, complementation tests were not performed).

When an insertion lies in the region of gene overlap, FlyBase uses the symbol of one gene in the P insertion symbol, and lists associated alleles for the other genes.

Table 2 shows the results of complementation tests with 18 stocks mapping recessive lethality to the P insertions. In these cases, strong arguments can be made for the lethality arising from disruption of the gene associated with the P element insertion based on noncomplementation with deletions and other mutations in the gene, or from the position of the P insertion relative to genic regions. For example, complementation tests with a deletion for the region of dachsous (ds) and a ds point mutation showed that the lethality of P{PZ}l(2)01855⁰¹⁸⁵⁵ is attributable to ds disruption. This allowed the insertion symbol to be revised to P{PZ}ds⁰¹⁸⁵⁵.

Table 2. Insertions causing lethal phenotypes.

Original Symbol	Noncomplementing Deletions and Mutations	Phenotype^a	Complementing Deletions	New Insertion Symbol
P{lacW}lola^k09901	lola⁰⁰⁶⁴², lola^ORC4	l	^bDf(3R)Exel6190, Df(3R)Exel6191
P{lacW}l(2)k00705^k00705	betaTub56D^YC0063, Df(2R)BSC782	l		P{lacW}betaTub56D^k00705
P{lacW}l(2)k05911^k05911	CG31728^f02493, Df(2L)BSC277, Df(2L)BSC768	l
P{PZ}l(2)00248⁰⁰²⁴⁸	Ef1alpha48D⁰¹²⁷⁵, Df(2R)BSC329, Df(2R)BSC879	l		P{lacW}EF1alpha48D⁰⁰²⁴⁸
P{lacW}l(2)k09848^k09848	CG7845^c00845, Df(2R)ED1482	l
P{PZ}l(2)01855⁰¹⁸⁵⁵	ds^UAO71, Df(2L)Exel8003	l		P{PZ}ds⁰¹⁸⁵⁵
P{lacW}l(2)k13905^k13905	Df(2L)glu-17C	l		P{lacW}Cyt-c-p^k13905
P{lacW}l(2)k14805^k14805	Adf1⁰¹³⁴⁹, Df(2R)ED1552	l		P{lacW}Adf1^k14805
P{PZ}l(2)03563⁰³⁵⁶³	Df(2R)BSC668, Df(2R)ED2354	l		P{PZ}Oaz⁰³⁵⁶³
P{PZ}l(2)05287⁰⁵²⁸⁷	CG12050^KG03759, Df(2L)BSC302, Df(2L)Exel7080	l
P{lacW}l(2)k10502^k10502	Letm1^MB02246, Df(2R)ED4061	pl		P{lacW}Letm1^k10502
P{lacW}LeuRS^SH0501	LeuRS^c03210, Df(2L)drm-P2	l
P{lacW}Ranbp11^SH0971	Ranbp11^B217, Df(2R)BSC398	l
P{lacW}Arpc4^SH1036	Arpc4^e00819, Df(2L)Exel6015	l
P{lacW}bsf^SH1181	Df(2L)BSC149, Df(2L)Exel8038	l
P{lacW}l(2)08770^k04808	Ttd14^EY01823, Ttd14^KG03769, Df(2R)BSC335	l/pl		P{lacW}Ttd14^k04808
P{PZ}l(2)08770⁰⁸⁷⁷⁰	Ttd14^KG03769	l		P{PZ}Ttd14⁰⁸⁷⁷⁰
P{PZ}l(2)10685¹⁰⁶⁸⁵	^cDf(2L)Exel6004, Df(2L)ED108	pl

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Phenotype in complementation tests: l, lethal; pl, partially lethal; l/pl, lethal in combination with deletion and partially lethal in combination with other insertions.

Results map lethality to lola in agreement with Bass et al. (2007), and not to region 94A as suggested by old sequence data.

Unpublished results from the Gene Disruption Project showed failure to complement P{lacW}l(2)10685^k00420 (http://flybase.org/reports/FBal0008159.html).

Table 3 shows the results of complementation tests with 44 P element stocks that indicate lethality maps to the P insertion itself or to a closely linked site. Confidence that a P insertion is responsible for a phenotype and that the phenotype is not attributable to a hit-and-run mutation tightly linked to the P insertion increases as the size of the interval defined by noncomplementing deletions decreases. Although past experience has shown that noncomplementation with any deletion strongly predicts that phenotypes are caused by P insertions (Spradling et al. 1999), we cannot formally associate lethality with these insertions from our deletion crosses alone. For this reason, insertions within the transcribed regions of genes have been renamed to reflect their physical position, separate alleles have been named to represent the recessive lethality, and the respective FlyBase entries indicate (in the Notes on Origin section of allele reports, and the Comments section of insertion reports) that the insertion and the lethal locus may represent the same mutational event. For example, the insertion formerly called P{lacW}l(2)k08601^k08601 lies within the Mef2 transcription unit. The insertion is now denoted by P{lacW}Mef2^k08601, the coincident or closely linked recessive lethal mutation is denoted l(2)k08601^k08601, and FlyBase entries indicate the two genetic elements may be the same entity. We made 28 such changes (Table 3, top section). No symbol updates were needed for nine other insertions within the transcribed portions of genes (Table 3, middle section). The seven insertions that lie outside the transcribed portions of genes (Table 3, bottom section) retain their original insertion names, because it is standard practice for FlyBase not to represent such insertions with separate symbols for insertions and lethal loci.

Table 3. Insertions with coincident or closely linked lethal mutations.

Original Symbol	Noncomplementing Deletions and Mutations	Phenotype^a	New Insertion Symbol	New Allele Symbols^b	New Lethal Allele
Insertion and lethality may not be separable, but separate insertion and lethal locus named
P{lacW}l(2)SH0499^SH0499	Df(2R)BSC334, Df(2R)Exel7153	v-l	P{lacW}MED9^SH0499	CG42518^SH0499	l(2)SH0499^SH0499
P{lacW}l(2)45Ai^k00116	Df(2R)BSC271	l	P{lacW}CG8078^k00116		l(2)45Ai^k00116
P{lacW}l(2)k02206^k02206	Df(2R)BSC402	l	P{lacW}CG33785^k02206	CG33786^k02206	l(2)k02206^k02206
P{lacW}l(2)k03201^k03201	Df(2L)BSC296, Df(2L)BSC354	l	P{lacW}Sec61alpha^k03201		l(2)k03201^k03201
P{lacW}l(2)k04003k⁰⁴⁰⁰³	Df(2L)ED623	l	P{lacW}Trs23^k04003		l(2)k04003^k04003
P{lacW}l(2)k04308^k04308	Df(2R)BSC281, Df(2R)BSC303	l	P{lacW}gem^k04308		l(2)k04308^k04308
P{lacW}l(2)k05448^k05448	Df(2L)BSC245, Df(2L)BSC290, Df(2L)Exel6034	l	P{lacW}CG5776^k05448		l(2)k05448^k05448
P{lacW}l(2)k06204^k06204	Df(2R)BSC158, ^cl(2)k06205^k06205	l	P{lacW}Sec24AB^k06204	CR45467^k06204	l(2)k06204^k06204
P{lacW}l(2)k06205^k06205	Df(2R)BSC158, ^cl(2)k06204^k06204	l	P{lacW}Sec24AB^k06205	CR45467^k06205	l(2)k06204^k06205
P{lacW}l(2)k06502^k06502	Df(2L)ED270	l	P{lacW}CG11030^k06502		l(2)k06502^k06502
P{lacW}l(2)k07215^k07215	Df(2L)BSC312, Df(2L)BSC302, Df(2L)Exel6047	l	P{lacW}CG9246^k07215		l(2)k07215^k07215
P{lacW}l(2)k07408^k07408	Df(2R)BSC359	l	P{lacW}AsnRS-m^k07408		l(2)k07408^k07408
P{lacW}l(2)k08601^k08601	Df(2R)X1	l	P{lacW}Mef2^k08601		l(2)k08601^k08601
P{lacW}l(2)k09328^k09328	Df(2R)ED2308	l	P{lacW}CG17574^k09328		l(2)k09328^k09328
P{lacW}l(2)k10105^k10105	Df(2L)BSC245	l	P{lacW}CG5287^k10105		l(2)k10105^k10105
P{lacW}l(2)k10239^k10239	Df(2L)Exel7077	l	P{lacW}sick^k10239		l(2)k10239^k10239
P{lacW}l(2)k10317^k10317	Df(2R)BSC360	l	P{lacW}MESK2^k10317		l(2)k10317^k10317
P{lacW}l(2)k12402^k12402	Df(2R)BSC280	l	P{lacW}prel^k12402		l(2)k12402^k12402
P{lacW}l(2)k13412^k13412	Df(2R)BSC279	l	P{lacW}CG8026^k13412	CG45085^k13412	l(2)k13412^k13412
P{lacW}l(2)k13604^k13604	Df(2L)ED21	l	P{lacW}CG3645^k13604		l(2)k13604^k13604
P{lacW}l(2)k16204^k16204	Df(2R)Exel7164	l	P{lacW}HnRNP-K^k16204		l(2)k16204^k16204
P{lacW}l(2)k16805^k16805	Df(2R)BSC668	l	P{lacW}Cpsf160^k16805		l(2)k16805^k16805
P{lacW}l(2)k17002^k17002	Df(2R)X58-12	l	P{lacW}CG13510^k17002	CG13511^k17002, CG42565^k17002	l(2)k17002^k17002
P{PZ}l(2)04008⁰⁴⁰⁰⁸	Df(2L)Exel6028	l	P{PZ}Ca-beta⁰⁴⁰⁰⁸		l(2)04008⁰⁴⁰⁰⁸
P{lacW}l(2)s4831^s4831	Df(2R)Exel7164	l	P{lacW}HnRNP-K^s4831		l(2)s4831^s4831
P{PZ}l(2)rG270^rG270	Df(2R)X58-12	l	P{PZ}Vps20^rG270		l(2)rG270^rG270
P{PZ}l(2)08492⁰⁸⁴⁹²	Df(2R)Exel6054, Df(2R)Exel7092	l	P{PZ}CG30493⁰⁸⁴⁹²	CG30496⁰⁸⁴⁹²	l(2)08492⁰⁸⁴⁹²
P{PZ}l(2)10481¹⁰⁴⁸¹	Df(2R)Kr10, Df(2R)bw^VDe2LPx^KR	pl	P{PZ}lov¹⁰⁴⁸¹		l(2)10481¹⁰⁴⁸¹
Insertion and lethality may not be separable, but separate insertion and lethal locus already existed.
P{lacW}CG30007^SH0071	Df(2R)BSC158	l
P{lacW}CG8414^SH0180	Df(2R)ED2457	l
P{lacW}ZnT49B^SH0360	Df(2R)BSC485, Df(2R)Exel7121	l
P{lacW}CG6094^SH0578	Df(2L)BSC210, Df(2L)Exel7048	l
P{lacW}CG9641^SH1104	Df(2L)ED206	l
P{lacW}x16^SH1297	Df(2L)BSC108, Df(2L)ED6569	l
P{lacW}IntS8^SH1314	Df(2R)BSC382	l
P{lacW}clumsy^SH1386	Df(2L)Exel6047	l
P{lacW}YL-1^SH1685	Df(2L)BSC145	l
Insertion not within the transcribed portion of a gene. Insertion and lethality may not be separable, but no separate lethal locus named.
P{lacW}l(2)k00302^k00302	Df(2L)BSC892	l
P{lacW}l(2)k07803^k07803	Df(2R)BSC298, Df(2R)B5	l
P{lacW}l(2)k09035^k09035	Df(2L)Exel6034	l
P{lacW}l(2)k11328^k11328	Df(2L)BSC277, Df(2L)BSC892, Df(2L)BSC290, Df(2L)ED784	l
P{lacW}l(2)k15817^k15817	Df(2L)BSC241	l
P{lacW}l(2)37Db^k16106	Df(2L)Exel6042	l
P{PZ}l(2)03996⁰³⁹⁹⁶	Df(2R)BSC268	l

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Phenotype in complementation tests: l, lethal; pl, partially lethal; v-l, homozygous viable but lethal in combination with deletions.

When an insertion lies in the region of gene overlap, FlyBase uses the symbol of one gene in the P insertion symbol and lists associated alleles for the other genes.

Original allele symbol.

Table 4 shows the results of complementation tests that allowed us to refine the mapping of 21 P insertions that had previously been mapped to polytene chromosome bands by in situ hybridization. Because we have no sequence localizations for these insertions, we cannot assign symbols reflecting their proximity to annotated genes. Consequently, they retain their original symbols indicating they are members of genetically defined, recessive lethal, or sterile complementation groups.

Table 4. Insertions with refined mapping.

Original Symbol	Noncomplementing Deletions	Phenotype^a	Complementing Deletions	Refined Mapping
P{PZ}ms(2)43C⁰⁰⁹¹⁹	Df(2R)ED1715, Df(2R)ED1673	ms		43A4–D3, 2R:7326951–7533553
P{A92}disd¹	Df(2R)BSC152, Df(2R)BSC298	l		46C1–7, 2R:9875312–9958120
P{A92}hall¹	Df(2R)BSC334, Df(2R)ED3610	l		55B2–C4, 2R:18051197–18357037
P{lacW}l(2)35Fg^k08106a	Df(2L)ED1102	l	Df(2L)Exel7066	36A1–36A10; 2L:16457328–16684883
P{SUPor-P}l(2)55Db^425-1	Df(2R)BSC335	l		55C6–F1, 2R:18398361–18755764
P{PZ}l(2)37Ad^02660b	Df(2L)Exel6042, Df(2L)OD15, Df(2L)ED1202	l		37B8–10, 2L:18973942–19049265
P{lacW}l(2)43Bd^k13522	Df(2R)BSC263, Df(2R)ED1715	l	Df(2R)BSC264	43A4–B2, 2R:7326951–7395885
P{hsneo}fs(2)neo4¹	Df(2L)ED5878	l/fs	Df(2L)BSC106, Df(2L)ED19, Df(2L)ED50001	21B1–3, 2L:72671–159063
P{hsneo}fs(2)neo5¹	Df(2L)BSC150, Df(2L)Exel6049	l		40A5–D3, 2L:21828252–22019106
P{lacW}oho55DE^k13104	Df(2R)BSC399	l	Df(2R)Exel7157	55D1–E2, 2R:18503870–18621522
P{lacW}l(2)10685^k00420	Df(2L)Exel6004	l		21E4–F1, 2L:1074079–1158137
P{BS2.7B}l(2)32BCa¹³	Df(2L)BSC213	l	Df(2L)BSC241	32B1–C1, 2L:10809118–11001451
P{lacW}l(2)08492^k10320	Df(2R)Exel6054, Df(2R)Exel7092	l		43E9–12, 2R:7665795–7708707
P{lacW}l(2)05287^k16804b	Df(2L)BSC302, Df(2L)Exel7080	l		39A1–2, 2L:21070044–21102742
P{ry11}fs(2)ry6¹	Df(2L)BSC107	l/fs		21C2–E2, 2L:431096–574741
P{ry11}fs(2)ry11¹	Df(2L)BSC107	l/fs		21C2–E2, 2L:431096–574741
P{PZ}l(2)02836a^02836a	Df(2R)Exel6063	l		52F6–53C4, 2R:16187888–16386515
P{PZ}l(2)03832a^03832a	Df(2L)ED1466	l	^bDf(2L)BSC103	39E7–40A5, 2L:21676769–21828548
P{PZ}l(2)04535b^04535b	Df(2R)BSC326	l		42A14–C7, 2R:6236062–6746030
P{PZ}l(2)43Bb^04614a	Df(2R)BSC263	l	Df(2R)BSC264, Df(2R)ED1715	42F2–43A4, 2R:7146864–7326951
P{lacW}l(2)k12502b^k12502b	Df(2R)Kr10	l		60F2–5, 2R:25061964–25288936

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Phenotype in complementation tests: l, lethal; l/fs, lethal with female sterile escapers; ms, male sterile.

Figure 2 in Han et al. (2003) suggests insertion lies to the right of Df(2L)BSC103.

In summary, we have clarified the basis for phenotypic effects seen in 178 P element insertion stocks in the Bloomington Stock Center collection. This has allowed us to give the stocks less ambiguous genotypes, and to revise several potentially misleading FlyBase entries. We expect this information to be valuable to Drosophila geneticists using these insertions in experiments examining the effects of disrupting specific gene regions.

Supplementary Material

HTML Page - index.htslp

supp_6_8_2665__index.html^{(882B, html)}

Acknowledgments

The authors gratefully acknowledge the support and advice of Annette Parks, Kathy Matthews, Thom Kaufman, and Steven Marygold. L.K. and K.R.C. were supported by National Institutes of Health/Office of the Director (NIH/OD) grant P40 OD018537 to the Bloomington Drosophila Stock Center. G.H.M. was supported by NIH/National Human Genome Research Institute grant U41 HG000739 to the FlyBase Consortium.

Footnotes

Supplemental material is available online at www.g3journal.org/lookup/suppl/doi:10.1534/g3.116.030940/-/DC1

Communicating editor: A. Bashirullah

Literature Cited

Ashburner M., Golic K. G., Hawley R. S., 2005. Drosophila: A Laboratory Handbook. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY. [Google Scholar]
Bass B. P., Cullen K., McCall K., 2007. The axon guidance gene lola is required for programmed cell death in the Drosophila ovary. Dev. Biol. 304: 771–785. [DOI] [PMC free article] [PubMed] [Google Scholar]
Cooley L., Kelley R., Spradling A. C., 1988. Insertional mutagenesis of the Drosophila genome with single P-elements. Science 239: 1121–1128. [DOI] [PubMed] [Google Scholar]
Deak P., Omar M. M., Saunders R. D. C., Pal M., Komonyi O., et al. , 1997. P-element insertion alleles of essential genes on the third chromosome of Drosophila melanogaster: correlation of physical and cytogenetic maps in chromosomal region 86E–87F. Genetics 147: 1697–1722. [DOI] [PMC free article] [PubMed] [Google Scholar]
Han Y. G., Kwok B. H., Kernan M. J., 2003. Intraflagellar transport is required in Drosophila to differentiate sensory cilia but not sperm. Curr. Biol. 13: 1679–1686. [DOI] [PubMed] [Google Scholar]
Kania A., Salzberg A., Bhat M., D’Evelyn D., He Y., et al. , 1995. P-element mutations affecting embryonic peripheral nervous system development in Drosophila melanogaster. Genetics 139: 1663–1678. [DOI] [PMC free article] [PubMed] [Google Scholar]
Roch F., Serras F., Cifuentes F. J., Corominas M., Alsina B., et al. , 1998. Screening of larval/pupal P-element induced lethals on the second chromosome in Drosophila melanogaster: clonal analysis and morphology of imaginal discs. Mol. Gen. Genet. 257: 103–112. [DOI] [PubMed] [Google Scholar]
Salzberg A., Prokopenko S. N., He Y., Tsai P., Pal M., et al. , 1997. P-element insertion alleles of essential genes on the third chromosome of Drosophila melanogaster: Mutations affecting embryonic PNS development. Genetics 147: 1723–1741. [DOI] [PMC free article] [PubMed] [Google Scholar]
Spradling A. C., Stern D., Beaton A., Rhem E. J., Laverty T., et al. , 1999. The Berkeley Drosophila genome project gene disruption project. Single P-element insertions mutating 25% of vital Drosophila genes. Genetics 153: 135–177. [DOI] [PMC free article] [PubMed] [Google Scholar]

Associated Data

This section collects any data citations, data availability statements, or supplementary materials included in this article.

Supplementary Materials

HTML Page - index.htslp

supp_6_8_2665__index.html^{(882B, html)}

supp_g3.116.030940_TableS1.xlsx^{(21.8KB, xlsx)}

Data Availability Statement

Changes to FlyBase entries have been coordinated with this report and will appear in a 2016 FlyBase update. Strains may be obtained from the Bloomington Drosophila Stock Center.

[bib1] Ashburner M., Golic K. G., Hawley R. S., 2005. Drosophila: A Laboratory Handbook. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY. [Google Scholar]

[bib2] Bass B. P., Cullen K., McCall K., 2007. The axon guidance gene lola is required for programmed cell death in the Drosophila ovary. Dev. Biol. 304: 771–785. [DOI] [PMC free article] [PubMed] [Google Scholar]

[bib3] Cooley L., Kelley R., Spradling A. C., 1988. Insertional mutagenesis of the Drosophila genome with single P-elements. Science 239: 1121–1128. [DOI] [PubMed] [Google Scholar]

[bib4] Deak P., Omar M. M., Saunders R. D. C., Pal M., Komonyi O., et al. , 1997. P-element insertion alleles of essential genes on the third chromosome of Drosophila melanogaster: correlation of physical and cytogenetic maps in chromosomal region 86E–87F. Genetics 147: 1697–1722. [DOI] [PMC free article] [PubMed] [Google Scholar]

[bib5] Han Y. G., Kwok B. H., Kernan M. J., 2003. Intraflagellar transport is required in Drosophila to differentiate sensory cilia but not sperm. Curr. Biol. 13: 1679–1686. [DOI] [PubMed] [Google Scholar]

[bib6] Kania A., Salzberg A., Bhat M., D’Evelyn D., He Y., et al. , 1995. P-element mutations affecting embryonic peripheral nervous system development in Drosophila melanogaster. Genetics 139: 1663–1678. [DOI] [PMC free article] [PubMed] [Google Scholar]

[bib7] Roch F., Serras F., Cifuentes F. J., Corominas M., Alsina B., et al. , 1998. Screening of larval/pupal P-element induced lethals on the second chromosome in Drosophila melanogaster: clonal analysis and morphology of imaginal discs. Mol. Gen. Genet. 257: 103–112. [DOI] [PubMed] [Google Scholar]

[bib8] Salzberg A., Prokopenko S. N., He Y., Tsai P., Pal M., et al. , 1997. P-element insertion alleles of essential genes on the third chromosome of Drosophila melanogaster: Mutations affecting embryonic PNS development. Genetics 147: 1723–1741. [DOI] [PMC free article] [PubMed] [Google Scholar]

[bib9] Spradling A. C., Stern D., Beaton A., Rhem E. J., Laverty T., et al. , 1999. The Berkeley Drosophila genome project gene disruption project. Single P-element insertions mutating 25% of vital Drosophila genes. Genetics 153: 135–177. [DOI] [PMC free article] [PubMed] [Google Scholar]

PERMALINK

Phenotypes Associated with Second Chromosome P Element Insertions in Drosophila melanogaster

Lily Kahsai

Gillian H Millburn

Kevin R Cook

Abstract

Materials and Methods

Data availability

Results and Discussion

Table 1. Insertions with no associated lethal or sterile phenotype.

Table 2. Insertions causing lethal phenotypes.

Table 3. Insertions with coincident or closely linked lethal mutations.

Table 4. Insertions with refined mapping.

Supplementary Material

Acknowledgments

Footnotes

Literature Cited

Associated Data

Supplementary Materials

Data Availability Statement

ACTIONS

PERMALINK

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Cite

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PERMALINK

Phenotypes Associated with Second Chromosome P Element Insertions in Drosophila melanogaster

Lily Kahsai

Gillian H Millburn

Kevin R Cook

Abstract

Materials and Methods

Data availability

Results and Discussion

Table 1. Insertions with no associated lethal or sterile phenotype.

Table 2. Insertions causing lethal phenotypes.

Table 3. Insertions with coincident or closely linked lethal mutations.

Table 4. Insertions with refined mapping.

Supplementary Material

Acknowledgments

Footnotes

Literature Cited

Associated Data

Supplementary Materials

Data Availability Statement

ACTIONS

PERMALINK

RESOURCES

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