Fig. 4.

Genomic evidence for the role of unequal exchange at the Bar locus. (A) Model for the origin of the B¹ allele by unequal exchange (17) between two different roo transposable elements (51). The distal and proximal segments of the B¹ duplication are shown in blue and orange, respectively, and roo elements are shown in green. (B) Genome annotation and depth of coverage for X chromosome balancers carrying B¹ (FM7a-785) and WT revertants (Binsc-107–614 and Binscy-107–624). Note the twofold increase in depth that starts downstream of B-H2 and ends upstream of CG12432 in the FM7a-785 chromosome carrying B¹ that is lacking in Binsc-107–614 and Binscy-107–624 revertants. (C) Model for the reversion of the B¹ allele to WT by unequal exchange between the two duplicated regions. The model shows an interchromosomal exchange event (15, 16); however, intrachromosomal exchange events are also possible (18, 19). (D) Schematic of sequence variants in B¹ chromosomes (FM7a-785) and WT revertants (Binsc-107–614 and Binscy-107–624). Sequences from the distal and proximal duplicated regions in B¹ chromosomes map to the same coordinates in the reference genome, resulting in apparent heterozygosity. The two revertant chromosomes are characterized by different haplotypes of homozygous SNPs. Sequences shared by both revertants at their 5′ and 3′ ends can be used to define the boundaries of unequal exchange events and partially phase the distal and proximal haplotypes, respectively. Diagnostic SNPs from fragments that span the junctions of putative unequal exchange events then can be used to phase haplotypes on both sides of both exchange junctions in the B¹ chromosomes (dotted arcs), which together with the sequence of the revertants can be used to assign the location of each exchange event to the appropriate revertant stock.