The Molecular and Genetic Characterization of Second Chromosome Balancers in Drosophila melanogaster

Abstract

Balancer chromosomes are multiply inverted and rearranged chromosomes used in Drosophila melanogaster for many tasks, such as maintaining mutant alleles in stock and complex stock construction. Balancers were created before molecular characterization of their breakpoints was possible, so the precise locations of many of these breakpoints are unknown. Here, we report or confirm the positions of the 14 euchromatic breakpoints on the 2^nd chromosome balancers SM1, SM5, CyO, and SM6a. This total includes three breakpoints involved in a complex rearrangement on SM5 that is associated with the duplication of two genomic regions. Unbiased sequencing of several balancers allowed us to identify stocks with incorrectly identified balancers as well as single and double crossover events that had occurred between 2^nd chromosome balancers and their homologs. The confirmed crossover events that we recovered were at least 2 Mb from the closest inversion breakpoint, consistent with observations from other balancer chromosomes. Balancer chromosomes differ from one another both by large tracts of sequence diversity generated by recombination and by small differences, such as single nucleotide polymorphisms (SNPs). Therefore, we also report loss-of-function mutations carried by these chromosomes and unique SNP and InDel polymorphisms present on only single balancers. These findings provide valuable information about the structure of commonly used 2^nd chromosome balancers and extend recent work examining the structure of X and 3^rd chromosome balancers. Finally, these observations provide new insights into how the sequences of individual balancers have diverged over time.

Balancer chromosomes are multiply inverted and rearranged chromosomes that both suppress recombination during meiosis and prevent the recovery of recombinant chromosomes. Balancers in Drosophila melanogaster are used for a number of tasks, such as maintaining deleterious alleles in stock, preserving linkage relationships among alleles, and allowing complex stock construction. Most balancers carry recessive lethal or sterile mutations that prevent them from becoming homozygous in stock, as well as dominant visible markers to make their inheritance easy to follow in crosses. Balancers are available for all chromosomes in D. melanogaster except the small 4^th chromosome, which does not normally undergo exchange, and the Y chromosome.

Because balancers were created before DNA sequencing was available, the precise locations of most inversion breakpoints and the nature of most of the marker alleles carried by balancers have remained unknown. Recently, the positions of most of the inversion breakpoints on the X chromosome balancer FM7 and the 3^rd chromosome balancers TM3, TM6, and TM6B were reported or confirmed (Miller et al. 2016a; b). These analyses revealed that several genes are disrupted by breakpoints including the highly conserved tumor suppressor gene p53, which was bisected by an inversion breakpoint on TM3 (Miller et al. 2016a).

Furthermore, whole-genome sequencing (WGS) of multiple X and 3^rd chromosome balancers revealed that large chromosomal segments had been exchanged with sequences from nonbalancer homologs by meiotic recombination. For example, double crossovers within an inverted segment of the X chromosome balancer FM7c led to loss of the female sterile allele sn^X2 on multiple occasions (Miller et al. 2016b). Likewise, double crossovers were reported within inverted segments of the 3^rd chromosome balancers TM3 and TM6B, and single-exchange events were found to be common in the unbalanced distalmost 7 Mb of chromosome arm 3L in TM3 (Miller et al. 2016a). There was also evidence that balancers had diverged at the nucleotide level since their common origins. Here, we present a similar analysis of sequence diversity for the commonly used 2^nd chromosome balancers SM1, SM5, SM6a, and CyO.

These four 2^nd chromosome balancers have their origins in two naturally occurring paracentric inversions of 2L and 2R that were on the same chromosome. This chromosome was first described by Ward (1923), who was studying the Curly (Cy¹) mutation (recently renamed Duox^Cy (Hurd et al. 2015)). She reported that this chromosome (later known as In(2L)Cy + In(2R)Cy) showed reductions in crossing over in each chromosome arm when heterozygous with normal chromosomes. Sturtevant (1926) proposed that these reductions in exchange were due to paracentric inversions and later (Sturtevant 1931) demonstrated that the gene order had indeed changed for 2L. A similar study by Graubard (1932) verified the presence of the paracentric inversion on 2R. By 1936, Calvin Bridges and Ju-Chi Li had confirmed the presence of the two inversions by polytene chromosome analysis and had mapped their breakpoints to 22D;33F for In(2L)Cy and 42A;58A for In(2R)Cy (cited in Morgan et al. 1936; Bridges 1937; and Bridges and Warren 1944). Ward also identified and described a mutation in cinnabar (cn²) on the In(2L)Cy + In(2R)Cy chromosome.

Although In(2L)Cy + In(2R)Cy can be used as a 2^nd chromosome balancer, it is not very effective because it still allows exchange with a normal sequence homolog, albeit at a reduced frequency (Ward 1923). In an attempt to create a better whole-chromosome balancer, SM1 was made by irradiating an In(2L)Cy + In(2R)Cy chromosome marked with al², Duox^Cy, cn², and sp² (Lewis and Mislove 1953). Polytene chromosome analysis revealed that irradiation had induced a large pericentric inversion with breakpoints at 22A and 60B. While the addition of an inversion reduced recombination substantially, SM1 still allows low levels of recombination, especially in the large region of 2R not disrupted by inversion breakpoints (Lindsley and Zimm 1992). To isolate a still better balancer, Mislove and Lewis (1955) repeatedly X-rayed SM1, introducing two additional inversions and a complex rearrangement. This balancer, called SM5, is marked with al², Duox^Cy, cn², lt^v, and sp², and is associated with good fertility and viability for a chromosome so extensively rearranged (12 euchromatic breakpoints and, as we will discuss below, at least 4 heterochromatic breakpoints). Unlike the other second chromosome balancers that are euploid, the complex rearrangement in SM5 resulted in the duplication of segments 42A to 42E and 58A to 58F (Mislove and Lewis 1955).

In 1956, Oster reported a new balancer obtained after irradiating males carrying In(2L)Cy + In(2R)Cy marked with Duox^Cy, dpy^lvI, pr¹, cn² (Oster 1956). This balancer is referred to as CyO (Lindsley and Zimm 1992). EMS treatment of CyO several years after it was created changed the weak allele cn² to cn^2P, a null allele now present on some, but not all, CyO chromosomes (Craymer 1980). Finally, SM6 was created through a series of single exchanges between CyO and SM1 (Craymer 1984). Two versions of SM6 were made: SM6a marked with al², Duox^Cy, dpy^lvI, cn^2P, and sp²; and SM6b, which carries the additional marker amos^Roi-1.

In this study, we report or confirm the genomic positions of a majority of the breakpoints present on SM1, SM5, CyO, and SM6a. We also identify two previously unannotated marker mutations carried by these chromosomes and precisely define the two large duplicated segments carried by SM5. Furthermore, we find many novel loss-of-function mutations that are both shared and unique among this sample of balancers, demonstrating that, as seen with previous studies of balancers, significant genetic diversity exists among balancer chromosomes derived from single original isolates.

Although significant sequence diversity due to recombination has been observed among different versions of the X chromosome balancer FM7 and the 3^rd chromosome balancers TM3 and TM6B (Miller et al. 2016a; b), we find that, except for two single exchange events in the distal unbalanced region of 2R on CyO and SM5, few large tracts of sequence diversity exist on the SM5, CyO, or SM6a balancers. This suggests that all three of these balancers allow very little recombination with normal-sequence homologs and thus are near-complete balancers for the 2^nd chromosome. We do, however, identify several double crossovers within the SM1 chromosomes that we sequenced, indicating that, as previously reported, it is a poor balancer for a large portion of the right arm of the 2^nd chromosome (Lindsley and Zimm 1992). Finally, consistent with previous studies (Miller et al. 2016a; b), unbiased sequencing revealed four balancers that had been misidentified in stock genotypes.

Materials & Methods

Stocks used for breakpoint identification

All balancers sequenced in this study were obtained from stocks at the Bloomington Drosophila Stock Center (Table S1). Sequence data for four balancers from a previous study (Miller et al. 2016a) were also included. Before sequencing, multiple balancer-carrying males were crossed to multiple ISO-1 virgin females. ISO-1 is the Drosophila reference genome stock and was obtained in 2014 from the Berkeley Drosophila Genome Project (Hoskins et al. 2015).

DNA preparation and genome alignment

DNA for sequencing was prepared from balancer/ISO-1 males using the Qiagen DNeasy Blood and Tissue Kit. Flies were starved for 1 hr before freezing at –80°. Libraries were prepared and quantified as described in Miller et al. (2016a). All libraries were pooled, requantified, and sequenced in 150-bp paired-end mode on the Illumina NextSeq 500 instrument. Illumina Real Time Analysis version 2.4.6 was run to demultiplex reads and generate FASTQ files following sequencing. Alignment to the D. melanogaster reference genome (dm6) was performed using bwa version 0.7.15-r1140 (Li and Durbin 2009). SNPs were called using SAMtools version 1.5 and BCFtools version 1.4.1 (Li et al. 2009). DNA preparation, sequencing, and alignment for balancers from stocks 504, 22239, 24759 and the Hawley lab SM1 stock are described in Miller et al. (2016a).

Identification of balancer breakpoints

Breakpoints were identified as in Miller et al. (2016a). Briefly, split and discordant read pairs were isolated using SAMBLASTER (Faust and Hall 2014) from regions where rearrangements were previously reported to be present (Lindsley and Zimm 1992). Split and discordant pairs were then de novo assembled and BLAST was used to identify assembled fragments that aligned to two distinct regions of the genome. Breakdancer was used to validate our custom analysis and to search for novel rearrangements (Chen et al. 2009).

PCR and Sanger sequencing

Primers for PCR validation were designed using Primer3 (Rozen and Skaletsky 2000). Six of 10 inversion breakpoints in which the molecular position was confirmed or identified in this study were validated using PCR and Sanger sequencing (Table S2). Briefly, ExTaq polymerase was used according to the manufacturer’s instructions. Extension times and annealing temperature for each breakpoint are given in Table S2.

Identification of shared and unique SNPs

Shared and unique SNPs were identified using VCFtools version 0.1.15 (Danecek et al. 2011). Only SNPs with VCF quality scores >220 were considered for analysis. VCF files were merged using vcf-merge (part of the VCFtools package), which allowed the counting of shared and unique SNPs. SnpEff version 4.3p (Cingolani et al. 2012) was used to annotate VCF files. Filtering of annotated VCF files was done using custom scripts.

Complementation testing

Fly crosses were made on standard medium and reared under routine conditions (details provided on request). Crosses listed in Table S3 evaluated recessive phenotypes associated with balancer breakpoints. Stocks used to evaluate breakpoints were tested with the control crosses listed in Table S4. Genotypes and the sources of stocks are given in Table S1.

Testis dissection and microscopy

Flies for microscopy were grown on Ward’s Instant Drosophila Medium and maintained at 25°. dpy^ov1wg^Sp-1/SM5 males were crossed to Df(2L)Exel6005/CyO females and male offspring with genotype Df(2L)Exel6005/SM5 were selected and used for testis dissections. dpy^ov1wg^Sp-1/Df(2L)Exel6005 males were used as a control. Testes were dissected in TB1 buffer (15 mM 1:1 K₂HPO₄:KH₂PO₄, pH 6.7, 80 mM KCl, 16 mM NaCl, 5 mM MgCl₂, 1% PEG 6000) on a microscope slide. A coverslip was placed on the dissection and excess buffer was drained slowly using a Kimwipe. Samples were visualized and documented using the phase-contrast setting of an Olympus BX60 Upright Compound Microscope equipped with an Olympus DP73 Color Camera.

Data availability

All stocks are available from the Bloomington Drosophila Stock Center, with the exception of the Hawley lab SM1; TM3 stock, which is available upon request. Raw sequencing data for all samples have been uploaded to the National Center for Biotechnology Information (NCBI) at http://ncbi.nlm.nih.gov and can be found under BioProject PRJNA413446. Sequencing data for balancers from stocks 504, 22239, 24759 and the Hawley lab SM1 stock were submitted to NCBI previously and can be found under BioProject PRJNA315473. Scripts used to align data, call SNPs, create heatmaps, and identify shared and unique mutations are available on Github: https://github.com/danrdanny/2ndChromosomePaper. Original data underlying this manuscript can be accessed from the Stowers Original Data Repository at http://www.stowers.org/research/publications/libpb-1257.

Results

Sequencing and identification of inversion breakpoints

To identify the breakpoints carried by the 2^nd chromosome balancers SM1, SM5, CyO, and SM6a, we crossed 18 stocks carrying one of these balancers to the Drosophila reference genome stock, ISO-1, and selected balancer/ISO-1 males for WGS. We also analyzed data from four 2^nd chromosome balancers sequenced previously (Miller et al. 2016a) (Table 1). Among this panel of 22 balancer chromosomes, we identified four cases where balancers had been incorrectly identified in the original stocks (Table 1). Throughout the text we refer to the mislabeled stocks by their stock numbers and group them with their correct balancer chromosome in figures.

Table 1. Balancer stocks used in this study.

Stock number1	Genotype	Label	Actual
223	ap4/SM5	SM5	—
240	nwB/SM5	SM5	—
325	l(2)39a1 px1 slt1 sp1/SM5	SM5	SM1
400	sm1 px1 pd1/SM5	SM5	—
405	dpyov1 wgSp-1/SM5	SM5	—
1143	Df(2R)en28/SM5	SM5	—
1465	Df(2R)Dll-MP/SM6a	SM6a	—
6853	y1 w67c23; Df(2R)01D01W-L053/SM6a	SM6a	—
8785	y1 w*; sax5/SM6a	SM6a	CyO
9162	Rca1IX cn1 bw1/SM6a	SM6a	—
23663	w1118; Df(2L)BSC278/SM6a	SM6a	—
24380	w1118; Df(2R)BSC356/SM6a	SM6a	—
Hawley lab stock1	wgSp-1/SM6a; Pri1 Dr1/TM3, Sb1 Ser1	SM6a	SM1
2	w*; betaTub60D2 KrIf-1/CyO	CyO	—
31	w118; Df(2R)H3D3/CyO	CyO	—
471	BkdM/CyO	CyO	—
5041	amd21 Bl1/CyO; DCTN1-p1501/TM3, Sb1 Ser1	CyO	—
533	stil3/CyO	CyO	—
1602	Df(2L)TW65/CyO	CyO	—
3076	Df(2L)E55, rdo1 hook1 LarE55 pr1/CyO	CyO	—
222391	y1 w*; P{y+t7.7 = Mae-UAS.6.11}Dpit47LA00491/CyO; l(3)**/TM3, Sb1 Ser1	CyO	—
247591	w*; snaSco/CyO; P{w+mC = ninaD-GAL4.W}3/TM3, Sb1	CyO	SM1

¹2^nd chromosome balancers sequenced as part of Miller et al. 2016a are indicated after their stock number.

Previous studies based on polytene squashes reported the presence of 14 euchromatic breakpoints and one heterochromatic breakpoint on the SM1, SM5, CyO, and SM6a balancer chromosomes (Table 2; Figure 1) (summarized in Lindsley and Zimm 1992). Eleven of the euchromatic breakpoints as well as the heterochromatic breakpoint are associated with simple inversions. The remaining three euchromatic breakpoints are associated with the complex rearrangement on SM5 that duplicated two genomic regions: 42A7–42E1 and 58A4–59A2 (Table 2).

Table 2. Breakpoints on 2^nd chromosome balancers.

Balancer(s)	Component aberration	Polytene breakpoint1	Proximal breakpoint coordinate	Distal breakpoint coordinate	Duplication (+) or deletion (–)	Predicted band2	Disrupts
SM1, SM5, SM6a, CyO	In(2L)Cy	22D1–2	Unknown3	Unknown3	Unknown	22D1	CG11723, TBCD, or AIF4
		33F5–34A1	Unknown5	Unknown5	Unknown	33F4	MRP
SM1, SM5, SM6a, CyO	In(2R)Cy	42A2–3	2R:6,012,459	2R:6,012,739	+280	42A7	5′ of Src42A
		58A4–58B1	2R:21,971,918	2R:21,972,072	−153	58A4
SM1, SM5, SM6a	In(2LR)SM1	22A3–22B1	2L:1,586,845	2L:1,586,840	−4	22A3	haf, CG10869
		60B–60C	2R:24,117,046	2R:24,117,059	−12	60B11	CG3257
SM6a, CyO	In(2LR)O	30E–30F	2L:9,805,575	2L:9,805,567	−7	30D1	nAChRα6
		50C10–50D1	2R:14,067,771	2R:14,067,782	−10	50D4	Prosap
SM5	In(2L)SM5-16	21D1–2	2L:675,187	2L:675,190	+4	21E2	ds
		36C	2L:16,995,337	2L:16,995,336	+2	36B6
SM5	In(2L)SM5-26	29C–29E	Unknown7	Unknown7	Unknown	29D5–E48	Unknown
		40F	Unknown	Unknown	Unknown	Unknown	Unknown
SM5	Dp(2;2)SM56	42D	Unknown9	6,917,406	Unknown	42E1	CG3015810
		53C	2R:16,682,351	2R:16,682,827	−475	53D1	CG30463
		58F	2R:22,689,962	2R:22,689,962	0	59A2	CR4476311

¹Breakpoint observed in polytene chromosome preparations (Lindsley and Zimm 1992).

²Breakpoint position predicted from genomic coordinate using FlyBase correlation table.

³Breakpoint mapped to the interval 2L:2,146,403–2,156,403.

⁴One or none of these three genes may be affected by the breakpoint.

⁵Breakpoint mapped to the interval 2L:12,726,221–12,736,221.

⁶Because SM5 arose from SM1 through two inversions (In(2L)SM5-1 followed by In(2L)SM5-2) and a complex rearrangement, we have given symbols to these component aberrations to replace the single aberration In(2LR)SM5. The symbol Dp(2;2)SM5 was chosen for the complex rearrangement to emphasize the duplicated segment from the progenitor over the inverted segment.

⁷This breakpoint could not be localized molecularly, but recessive lethality presumably associated with the breakpoint was mapped to the interval 2L:8,529,124–8,700,124 by complementation tests with molecularly defined chromosomal deletions.

⁸Bands corresponding to the 2L:8,529,124–8,700,124 interval defined by chromosomal deletions.

⁹The proximal side of the breakpoint is present in two presumably identical copies juxtaposed to low-complexity sequence and maps to the 2L:6,916,809–6,917,405 interval.

¹⁰The sequence on the distal side of the breakpoint suggests this gene is disrupted.

¹¹A second, intact copy of this gene is present elsewhere on SM5.

Figure 1.

Second chromosome balancer inversion breakpoints and rearrangements. Chromosome bands here and in the text are those predicted from the genomic coordinates of breakpoints in Table 2. (A) Breakpoints whose genomic positions are known are shown as solid lines, those approximated (22D1 and 33F4) are shown as dashed lines, and those with unknown genomic coordinates (29D5–E4 and 40F) are shown as dotted lines. (B) Multiple rearrangements and inversions have resulted in novel configurations for each second chromosome balancer.

Using a combination of standard and large-insert libraries, we confirmed or identified the precise molecular positions of 8 of the 11 euchromatic inversion breakpoints (Table 2) and validated 6 of those using PCR and Sanger sequencing (Table S2). Although we were unable to identify the precise positions of three of these breakpoints (Table 2), we were able to map the two In(2L)Cy breakpoints in polytene bands 22D1 and 33F4 to within 10 kb using large-insert libraries. The exact position of the euchromatic 29D5–E4 breakpoint on SM5 was difficult to determine because the 40F breakpoint of the 29D5–E4 to 40F inversion lies in centric heterochromatin, making it challenging to analyze using either short-read or large-insert libraries. Nevertheless, we will present evidence below that it can be localized to the 16-gene interval 2L:8529124–8700124 corresponding to 29D5E4.

The complex rearrangement on SM5 (Dp(2;2)SM5) that duplicated 42A7–42E1 and 58A4–59A2 is shown in Figure 2. From the order and orientations of chromosomal segments in SM5, it is apparent this rearrangement was induced on an SM1 chromosome that already had two additional inversions (In(2L)SM5-1 and In(2L)SM5-2) (Table 2, Figure 2C). Euchromatic breaks in 42E1, 53D1 and 59A2 were involved to invert the 42E1–53D1 segment and insert a second copy of a segment from the progenitor chromosome that spanned an existing inversion breakpoint and comprised two subsegments (42E1–42A7 and 52A4–59A2) (Figure 2B) (Mislove and Lewis 1955; Lindsley and Zimm 1992). Our sequencing showed the presence of low-complexity sequences juxtaposed to the distal ends of both 42A7–42E1 segments, and they provide a clue to how the unusual mirror-image arrangement of segments may have arisen. They suggest the distal end of the 42A7–42E1 segment in the progenitor was first joined to a heterochromatic region and then, after replication, breaks within the heterochromatic region on sister chromatids joined to produce the mirrored configuration. The exact overall configuration of the intermediate rearrangement is not clear, but it likely involved inversion of the 42E1–53D1 segment as well. The low-complexity sequences made it difficult to determine the exact distal extent of the 42A7 to 42E1 segments (Table 2), and to know if there are sequences deleted or duplicated relative to the distal side of the 42E1 breakpoint. We determined the minimal extent of the duplicated 42A7 to 42E1 segment to be 2R:6,012,459–6,916,809 (Table 3; Figure 2A), an interval containing 83 protein-coding genes, 14 non-protein-coding (CR) genes, and 19 tRNA genes (r6.17 annotations) (Table S5). In contrast, it was relatively straightforward to characterize the 42E1;53D1 and 53D1;59A2 junctions, which flank the inverted segment and join it to the duplicated segment. Depth of coverage analysis allowed us to determine the precise extent of the duplicated 58A4 to 59A2 segment to be 2R:21,972,072–22,689,962 (Table 3, Figure 2A), an interval containing 117 protein-coding genes, 18 CR genes, and 6 snoRNA genes (Table S5). Knowing exactly which genes are duplicated is valuable for the construction of stocks. For example, SM5 has been used to maintain deficiencies of the haploinsufficient locus M(2)58F, which corresponds to RpS24 and/or RpS16, two genes contained within the 58A4 to 59A2 duplicated segment (Marygold et al. 2007).

Figure 2.

SM5 carries a complex rearrangement that duplicates two chromosomal segments. (A) Depth-of-coverage analysis of SM5 2R indicates that two regions on the standard map are duplicated (orange and blue boxes). The gray shaded area represents centric heterochromatin, which appears heterogeneous due to the difficulty of aligning short-read data to repetitive sequences. (B) The two duplicated segments lie adjacent to one another on SM5. One segment (highlighted in orange) duplicates 42A7–42E1 while the other (highlighted in blue) duplicates 58A4–59A2. Note the mirror-image arrangement of the two segments present in two copies with heterochromatin (turquoise) separating them. The two duplicated segments are joined to the end of the 53D1–42E1 segment, which is inverted relative to the progenitor. (C) The 58A4;42A7 inversion breakpoint is present within the duplication on SM5 because it was present on the progenitor chromosome in the region that was duplicated (denoted by blue and orange boxes). The 42E1–53D1 interval was inverted as part of the complex rearrangement that is now present on SM5.

Table 3. Details of the duplicated segments on SM5.

Balancer	Start	End	Size	Predicted bands1
SM5	2R:6,012,459	2R:6,916,8092	904,350	42A7–42E1
	2R:21,972,072	2R:22,689,962	712,929	58A4–59A2

¹Breakpoint position predicted from genomic coordinates using FlyBase correlation table.

²This coordinate represents the minimal distal extent of this interval. The maximal extent is 2R:6,917,405.

Inversion breakpoints affect protein-coding genes

Several of the breakpoints we identified or confirmed lie within the transcribed regions of protein-coding genes (Table 2). Breakpoints that lie in intergenic regions and those we mapped to small intervals may also affect the activities of genes. To test the breakpoints for strong phenotypic effects, we performed complementation tests with deficiencies spanning these breakpoints and scored for lethality, female sterility, or grossly abnormal morphology (Table S6). Only two of the breakpoints, 21E2 and 29D5–E4 on SM5, gave phenotypes in these tests. The 21E2 breakpoint in the gene dachsous (ds) was lethal, with the few escapers having the short appendages typical of ds mutants, consistent with previous reports (Craymer 1980; Clark et al. 1995). The 29D5–E4 breakpoint on SM5 also appears to be lethal. Four deletions chosen to span the region of the breakpoint defined by polytene chromosome analysis (29C–E; (Lindsley and Zimm 1992)) were all lethal in combination with SM5. Assuming that the inversion breakpoint is the only lethal mutation present, it maps to the 16-gene region common to all the deletions (2L:12,726,221–12,736,221), which corresponds to 29D5–E4. While the 30D1 breakpoint disrupting nAChRα6 on SM6a and CyO is not associated with lethality or female sterility, previous studies showed that it and other loss-of-function nAChRα6 mutations confer insecticide resistance (Perry et al. 2007; Watson et al. 2010).

We were unable to evaluate the phenotypic effects of two breakpoints. The 59A2 breakpoint of the complex rearrangement on SM5 disrupts CR44763, but an intact copy is present elsewhere on SM5. The 42E1 breakpoint of the complex rearrangement appears to disrupt CG30158, because the sequence of the 42E1–53D1 junction shows that the break lies at 2R:6,917,406 within an intron. Nevertheless, the difficulties we encountered in characterizing the 42E1 ends of the mirror-image 42A7–42E1 segments leave us unable to say with certainty that they terminate at the same site. If, as we expect, the break is not unusually complicated and CG30158 is disrupted, our complementation tests (Table S6) indicate that knocking out CG30158 has no severe consequences.

Although it did not confer lethality or female sterility in complementation tests, the 22A3 breakpoint on SM1, SM5, and SM6a bisects the gene CG10869, which is expressed only in adult testes (Chintapalli et al. 2007). Complementation testing of SM5 with Df(2L)Exel6005, which encompasses CG10869, showed that males were sterile and that sperm failed to individualize during spermatogenesis (Figure 3). Consequently, we have renamed this gene no individualized sperm (nis). Although nis lies within an intron of hattifattener (haf), it is unlikely that disruption of haf contributes to male sterility, because haf shows negligible expression in the testis (Chintapalli et al. 2007). We did not examine SM5/Df(2L)Exel6005 flies for the incompletely penetrant muscle innervation defects seen when haf expression is reduced by RNAi or mutations (Kurusu et al. 2008).

Figure 3.

Spermatogenesis phenotypes from disrupting CG10869. The noncomplementation of Df(2L)Exel6005 and the SM5 inversion breakpoint in CG10869 results in recessive male sterility and degradation of late elongation-stage spermatid bundles. Phase-contrast micrographs of live squashed testis preparations from (A–F) Df(2L)Exel6005/dpy^ov1 wg^Sp-1 (indistinguishable from wild type) and (G–L) Df(2L)Exel6005/SM5 males. (A, G) Mitochondria are phase dark, small, and diffuse throughout the cytoplasm in primary spermatocytes (arrows denote mitochondria). (B, H) After meiosis, mitochondria aggregate and fuse beside each phase light nucleus, forming the nebenkern (arrows denote nebenkern), which appears normal in testes from Df(2L)Exel6005/SM5 males. (C, D, I, J) The nebenkern unfurls, and mitochondrial derivatives appear to elongate normally beside the growing flagellar axoneme during early elongation stages (arrows denote elongating mitochondrial derivatives). Cysts of 64 spermatids elongate together in smooth bundles (E) and later individualize (F) in the control, while Df(2L)Exel6005/SM5 spermatid bundles (K) appear vacuolated (arrow), suggesting tissue degradation, and sperm fail to individualize (L). The syncytial appearance of cells in many panels is a well-known artifact of live testis squash preparations in which ring canals between cells in a cyst are often broken open. Scale bar, 10 µm.

That we were able to discover a previously unknown mutation and determine the role of an uncharacterized gene demonstrates the value of molecularly mapping the inversion breakpoints on these commonly used balancer chromosomes. Furthermore, knowledge of the genes disrupted by inversion breakpoints is useful for researchers studying those genes in terms of their choice of balancer.

Sequence diversity among 2^nd chromosome balancers

As seen in studies of X and 3^rd chromosome balancers (Miller et al. 2016a; b), stretches of unique SNPs indicate the occurrence of recombination events between balancers and nonbalancer homologs. To investigate how much sequence diversity, if any, exists among each of the four 2^nd chromosome balancers, we plotted the positions of SNPs that were unique among balancers of the same type and found very few large tracts on the SM5, CyO, and SM6a balancers (Figure 4 B-D). Two exchange events were observed at the distal tip of 2R: one on CyO from stock 504 (Figure 4C, Figure 5A) and one on SM5 from stock 240 (Figure 5B). The single crossover (SCO) on CyO occurred at approximately 2R:24,509,500, ∼2.5 Mb away from the distalmost 58A4 breakpoint. The SCO on SM5 occurred at approximately 2R:25,241,500, ∼1.1 Mb away from the distalmost 60B11 inversion breakpoint. What appears to be a double crossover (DCO) event on CyO from stock 31 (Figure 4C) is in reality a duplication event discussed below.

Figure 4.

Heatmaps of unique SNPs reveals sequence diversity among 2^nd chromosome balancers. (A) Extensive sequence diversity appears to exist on the right arm of the 2^nd chromosome among SM1 balancers from three stocks, indicating that these regions are susceptible to double crossover events. (B–D) Little sequence diversity exists among the SM5, CyO, and SM6a chromosomes sequenced, except for a single exchange event on the distal 2R tip of CyO from stock 504. One apparent double crossover event on CyO from stock 31 is actually a duplication. (E) Comparing SNPs present on all SM1 stocks to SM5, which SM5 carries the ancestral SM1 polymorphism profile, reveals that SM1 chromosomes from two stocks experienced double crossover events while SM1 from stock 325 did not.

Figure 5.

Single (SCO) and double (DCO) crossover events recovered in this study. (A) The SCO at the distal tip of CyO from stock 504 lies 2.5 Mb distal to the distalmost breakpoint at 58A4. (B) An SCO occurred approximately 30 kb from the 2R telomeric repeats on SM5 from stock 240. It is unclear whether this SCO was the result of a meiotic crossover or another kind of exchange. (C-D) The DCO exchanges in the SM1 chromosomes from stocks 24759 and the Hawley lab stock lie at least 2.3 Mb from the inversion breakpoints flanking the DCO.

Unlike the other three balancers, we did find extensive sequence diversity within one region of 2R among the three SM1 chromosomes sequenced (Figure 4A). This was not surprising, as it was previously noted that the large 16-Mb interval between the 42A7 and 58A4 inversion breakpoints is vulnerable to DCO events (Lindsley and Zimm 1992). It is possible that one of the three SM1 sequences is identical to the sequence of the original SM1 balancer and the other two sequences represent DCO events, or that all three sequences represent DCO events. To determine which scenario is correct, we compared the SNP distribution of each SM1 chromosome against SM5, which was created from SM1, and which we assume is an ancestral snapshot of SM1. This revealed that only the SM1 chromosomes from stock 24759 and the Hawley lab stock had experienced DCO events (Figure 4E, Figure 5C-D). That only two of the three SM1 chromosomes differed from SM5 suggests that the SM1 chromosome used to make SM5 carried the SNP profile of the original SM1 chromosome.

Interestingly, the crossovers giving rise to these DCOs on SM1 occurred at least 2.3 Mb away from the flanking inversion breakpoints (Figure 5C-D). This distance and the ∼2.5 Mb distance observed for the SCO on CyO from stock 504 are consistent with previous observations that found SCO events between the 3^rd chromosome balancer TM3 and a normal-sequence chromosome occurred no closer than ∼2 Mb to an inversion breakpoint (Miller et al. 2016a; b). The SCO that occurred ∼1.1 Mb from the distalmost breakpoint on 2R in SM5 from stock 240 is challenging to interpret in this regard. It lies approximately 30 kb from telomeric repeats, and a region with increased recombination was reported previously for a similar subtelomeric region of the X chromosome (Anderson et al. 2008). This SCO may reflect a similar region of increased recombination on 2R. Whether subtelomeric exchanges reflect normal meiotic recombination or events associated with the maintenance of chromosome ends remains unclear (Kern and Begun 2008).

Structural differences exist among balancer stocks

Unbiased sequencing of a large number of 2^nd chromosome balancers also allowed us to identify novel and unexpected structural events within each stock. For example, we sequenced six balancers from stocks with deficiencies (Table 1) and identified two novel duplications (Figure 6). The CyO in stock 1602 balances Df(2L)TW65, a deletion of 37F–39E (approximate coordinates 2L:19,675,000–21,700,000), and carries a novel 1.2-Mb tandem duplication with coordinates 2L:20,422,204–21,606,670. Stock 31 contained CyO balancing Df(2R)H3D3, a deletion of 44D–44F (approximate coordinates 2R:8,430,000–8,850,000), and it carried a novel 402-kb duplication with approximate coordinates 2R:8,376,000–8,777,700. This duplicated region carried polymorphisms not seen on any other CyO balancer, suggesting that it originated from a chromosome other than CyO (Figure 4C). Both its proximal and distal ends were bounded by low-complexity or repetitive sequence, making it difficult to determine using paired sequencing reads where it was positioned in the genome. Because the sequencing depth of the duplicated segment was 50% higher than background, the duplicated segment appears to have co-segregated with CyO in the outcross to ISO-1. Unfortunately, the Df(2R)H3D3 stock was rebalanced at the Bloomington Stock Center shortly after the sequence analysis, so follow-up mapping to prove CyO carried the duplication was impossible. Regardless, these observations show that there are unique structural variations within balancer stocks and that balancers themselves can carry duplications. Neither of these duplications contain any of the haploinsufficient genes cataloged by Cook et al. (2012), yet they both partially overlap corresponding deficiencies and restore many genes to their normal two copies, which likely explains why they were retained and why, in general, a balancer carrying a duplication can have a competitive advantage when it arises in a stock.

Figure 6.

Duplications present in stocks where a deficiency was maintained with a 2^nd chromosome balancer. (A) CyO from stock 1602 carries a 1.2-Mb tandem duplication (blue arrow) that partially covers the Df(2L)TW65 deficiency (orange shading). (B) Stock 31 had a 402-kb duplication (blue arrow) that may have been present on CyO. The SNPs present within this duplicated segment indicate that it did not come from the CyO chromosome itself, but from an unknown second chromosome. The gray shaded areas represent centric heterochromatin.

Marker alleles carried by 2^nd chromosome balancers

Whole-genome sequencing provides an opportunity to identify and define the molecular nature of marker alleles carried by balancer chromosomes. Among these four balancers, there are both shared and unique visible mutations, which may be used to differentiate the balancers. For example, SM1 is marked with al² Duox^Cy cn² sp², while SM5 carries those markers as well as ds⁵⁵ and lt^v, and SM6a is marked with al² Duox^Cy dpy^lvI cn^2P sp². Most CyO balancers, meanwhile, are marked with Duox^Cy dpy^lvI pr¹ cn², although some have cn^2P instead of cn² (Craymer 1980). Of these nine marker alleles, five (ds⁵⁵, Duox^Cy, pr¹, cn², and sp²) have been sequenced previously, and we were able to confirm the molecular nature of all five (Table 4) as well as the nature of the nAChRα6° mutation associated with insecticide resistance (Perry et al. 2007; Watson et al. 2010). We also identified molecular abnormalities in two (al² and lt^v) of the four previously unsequenced markers (al², dpy^lvI, lt^v, and cn^2P). Note, however, that lt^v is a variegating allele of lt, and it is possible that the 40F breakpoint in SM5 induces position-effect variegation rather than the variegation being attributable to the transposon insertion we identified. We were unable to determine the nature of the lesions in dpy^lvI and cn^2P.

Table 4. Marker alleles present on 2^nd chromosome balancers.

Balancers	Allele	Mutation
SM1, SM5, SM6a, CyO	DuoxCy	Nonsynonymous C-to-A mutation changing Gly 1505 to Cys, consistent with Hurd et al. (2015).
SM1, SM5, CyO	cn2	cn2 has two roo insertions: one with a 70-nt target site duplication (TSD) of 2R:7,784,487–7,784,556 that includes the 1st intron and 2nd exon of cn, and the other in the 1st intron of cn with a 6-nt TSD of 2R:7,784,682-7,784,687. Previously reported as an 8-kb insertion in cn (Warren et al. 1996).
SM6a, CyO	cn2P	cn2P was induced by EMS treatment (Craymer 1980), and is present on some CyO chromosomes and all SM6a and SM6b chromosomes. Using our dataset, we are unable to identify the difference between cn2 and cn2P.
SM1, SM5, SM6a	al2	Previously unknown. 10-nt deletion in 4th exon of al resulting in a frameshift. Deletion is from 2L:386,781–386,793. The deletion may be a single deletion or two deletions, as 3 nt of sequence aligns in multiple positions within the 13-nt interval.
SM1, SM5, SM6a	sp2	412 insertion in 5′ UTR of Dat. Previously known (Eric Spana, personal communication).
CyO	pr1	Previously reported 412 insertion at 2L:20,074,872 (Kim et al. 1996).
SM5	ds55	21D2–36C inversion breakpoint is in 1st intron of ds. Previously reported (Clark et al. 1995).
SM5	ltv	Previously unknown. Doc insertion at/near 2L:22,927,436, which may disrupt the splice acceptor site of the 6th exon. Alternatively, the variegating phenotype may be due to the 40F breakpoint, which may be near lt.
CyO	nAChRα6°	30F–50D inversion breakpoint is within an intron of nAChRα6. Previously reported (Perry et al. 2007).
CyO	dpylvI	Unknown.

Mutations that are shared by and unique among balancer chromosomes

Many balancer chromosomes were created using X-ray mutagenesis, which generated not only useful inversions but also unrecognized mutations. Furthermore, as balancers have been kept in stock, they have diverged from one another over time through the accumulation of de novo SNP and InDel polymorphisms. Finally, cn^2P was induced by EMS treatment, which undoubtedly increased the number of mutations present on balancers carrying this marker (Craymer 1980).

From the five SM5, nine CyO, and five SM6a balancers sequenced, we identified 234,623 high-quality SNPs shared by at least two of these three balancer types. (We did not include SM1 in this analysis because we felt that three stocks, two of which had experienced large DCO events, were not sufficient to determine accurately which mutations were shared or novel.) We used SnpEff (Cingolani et al. 2012) to determine how many of these SNPs affect genes (both protein-coding and noncoding) and found 35 nonsense mutations, 62 splice site mutations, 9 start-loss mutations, and 8,898 missense mutations (summary statistics in Table 5, list of all shared mutations in Table S7). We also found 1,558 high-quality SNPs shared only among all SM5 balancers, 13,888 shared only among all CyO balancers, and 20,567 shared only among all SM6a balancers. These polymorphisms also introduce nonsense, splice acceptor, and missense mutations that are unique to these chromosomes (Table 5, Table S7). For example, all CyO balancers we sequenced have nonsense mutations in 2 genes, CG33310 and CG31750, not present on any of the SM5 or SM6a balancers sequenced. Finally, we identified an average of 2,627 unique SNPs per individual balancer chromosome. These unique SNPs resulted in a total of 683 unique missense mutations, 10 unique splice site mutations, and 11 unique nonsense mutations among all the balancers we studied (Table 5, list of all unique mutations in Table S8). As an example, CyO from stock 1602 has a nonsense mutation in Nplp4 that is not observed on any other balancer. That there are many mutations affecting genes both shared and unique among balancer chromosomes demonstrates that stock-to-stock variability exists among balancers and this variability may impact the fitness of stocks or the interpretation of experimental results.

Table 5. Shared or unique mutations carried by 2^nd chromosome balancers.

	Mutation type
Balancer	Missense	Splice site	Nonsense	Start-loss
All SM5 only	49	0	1	0
All CyO only	548	2	2	0
All SM6a only	520	0	0	0
Shared among all balancers	8898	62	35	9
Present on only one balancer	683	10	11	0

Discussion

Whole-genome sequencing of balancer chromosomes provides several important types of information. For example, it can tell us whether a balancer carries any mutations aside from its marker alleles, whether it has acquired any additional structural variations such as duplications or deletions, and which of its regions have undergone crossing over. It can also help us determine the exact molecular locations of breakpoints, which are useful for understanding how breakpoints may directly or indirectly affect genes.

Knowledge of the exact positions of inversion breakpoints has important consequences for choosing the appropriate balancer for maintaining an allele in stock. Because these breakpoints often bisect or lie very close to genes, they can disrupt gene function or affect it by position-effect suppression. For example, the 15D3 inversion breakpoint on the FM7 balancer bisects the predicted peptidase gene CG45002 (Miller et al. 2016b), and the 84B1 inversion breakpoint on TM6B affects the regulatory region of Antp (Miller et al. 2016a). In this study, we report or confirm the exact or approximate positions of eleven euchromatic inversion breakpoints present on the 2^nd chromosome balancers SM1, SM5, CyO, and SM6a (Table 2) along with the positions of the three euchromatic breakpoints of the duplication-associated complex rearrangement on SM5 (Table 3). Knowing the exact genes carried by the duplicated segments is important for researchers studying genes in these intervals who may not realize that their gene of interest is present in three copies.

Moreover, we find that balancers are not immune to de novo structural variation that may provide selective advantages in stock. In our study, two out of six balancers maintained in stock over a deficiency were associated with a duplication covering a large portion of the deficiency (Figure 6). At least one, and possibly both, of these duplications arose after the chromosomes were placed in stock with the deficiency, confirming that copy-number variation arises frequently enough for such duplications to be a concern. This serves as a reminder that balancers kept in stock for long periods of time may carry unexpected structural variation that could affect experimental results.

By comparing WGS data of related balancer chromosomes, we can identify exchange events between a balancer and its normal sequence homolog. Balancers have previously been shown to experience SCO events within terminal, noninverted segments and DCO events within inverted segments (Miller et al. 2016a; b), and both types of exchange events were observed in this study as well (Figure 5). It is notable that, like exchange events that occurred between an internal region of the 3^rd chromosome balancer TM3 and normal-sequence homologs (Miller et al. 2016a), the non-subtelomeric exchange events observed in this study occurred at least 2 Mb from the nearest inversion breakpoint. This strengthens the conclusion that inversion breakpoints suppress exchange over distances of 2–3 Mb.

Similar to observations of single exchange events in the distal unbalanced region of the 3^rd chromosome balancer TM3, the 2^nd chromosome balancer CyO allows exchange near the tip of 2R (and may also allow single exchange events near the tip of 2L). We therefore suggest that mutations in the intervals distal to 22D1 on 2L and 58A4 on 2R be balanced with SM5—not with CyO. (However, SM6a or SM1 should work well to maintain mutations in the distal tip of 2R.) Even though an SCO event was observed in the distal portion of 2R on SM5, this extremely distal event occurred in the last 30–40 kb of the chromosome and affected only 5 genes. Thus, we still encourage the use of SM5 for balancing distal genes. We also recommend maintaining more than one independent culture of stocks where there is risk of losing mutations from exchange with balancers.

Finally, WGS also provides an opportunity to investigate both the shared and unique SNPs affecting gene function that are carried by balancer chromosomes. Here, we were able to confirm or molecularly characterize 7 of the 9 previously reported marker alleles carried by these four 2^nd chromosome balancers (Table 4). In addition to known visible markers, all chromosomes carry a number of other mutations, most of which remain uncharacterized phenotypically. A study by Araye and Sawamura (2013) reported the presence of novel recessive lethal mutations carried by two balancers maintained in their lab. They suggested that WGS should reveal additional novel mutations affecting gene function. We identified 97 nonsense and splice site mutations (Table 5) shared among all four balancers studied (Table S7) as well as 26 nonsense and splice site mutations (Table 5) that are either unique among a family of balancers (Table S7) or unique to a specific balancer (Table S8). Knowing the genes that are mutated on balancers is important for researchers working with a specific gene who may not realize the balancer chromosome they are using is creating a heteroallelic loss-of-function genotype.

Whole-genome sequencing using short-read technology has now been completed for the Drosophila X chromosome balancers FM7a and FM7c (Miller et al. 2016b); the 2^nd chromosome balancers SM1, SM5, CyO, and SM6a; and the 3^rd chromosome balancers TM3, TM6, and TM6B (Miller et al. 2016a). These studies have revealed surprising findings about the structures of these chromosomes, the mutations carried by them, and the sequence diversity that exists among them. Sequencing a panel of presumably identical balancer chromosomes has also added to our understanding of the mechanisms by which inversion breakpoints suppress exchange, demonstrating that studies of these commonly used genetic tools can provide insights into challenging biological questions.

Supplementary Material

Supplemental Material is available online at www.g3journal.org/lookup/suppl/doi:10.1534/g3.118.200021/-/DC1