Rare recombination events generate sequence diversity among balancer chromosomes in Drosophila melanogaster

TL;DR

This study reveals rare recombination events in Drosophila balancer chromosomes, showing sequence diversity and structural variations that impact their use in genetic experiments.

Contribution

It provides the first detailed molecular characterization of balancer chromosomes, identifying recombination-driven sequence divergence and structural changes.

Findings

Identified precise inversion breakpoints in FM7 chromosomes.

Discovered megabase-scale sequence divergence among FM7 stocks.

Evidence of rare double crossover events replacing alleles.

Abstract

Multiply inverted balancer chromosomes that suppress exchange with their homologs are an essential part of the genetic toolkit in Drosophila melanogaster. Despite their widespread use, the organization of balancer chromosomes has not been characterized at the molecular level, and the degree of sequence variation among copies of any given balancer chromosome is unknown. To map inversion breakpoints and study potential sequence diversity in the descendants of a structurally identical balancer chromosome, we sequenced a panel of laboratory stocks containing the most widely used X-chromosome balancer, First Multiple 7 (FM7). We mapped the locations of FM7 breakpoints to precise euchromatic coordinates and identified the flanking sequence of breakpoints in heterochromatic regions. Analysis of SNP variation revealed megabase-scale blocks of sequence divergence among currently used FM7 stocks. We present evidence that this divergence arose by rare double crossover events that replaced a female-sterile allele of the singed gene (sn[X2]) on FM7c with wild type sequence from balanced chromosomes, and propose that many FM7c chromosomes in the Bloomington Drosophila Stock Center have lost sn[X2] by this mechanism. Finally, we characterize the original allele of the Bar gene (B[1]) that is carried on FM7 and validate the hypothesis that the origin and subsequent reversion of the B1 duplication is mediated by unequal exchange. Our results reject a simple non-recombining, clonal mode for the laboratory evolution of balancer chromosomes and have implications for how balancer chromosomes should be used in the design and interpretation of genetic experiments in Drosophila.