The third chromosome of D. pseudoobscura is polymorphic for over 30 different gene arrangements that were generated through a series of overlapping paracentric inversions. The frequencies of gene arrangements vary among geographic populations and over seasons suggesting that selection has acted on the polymorphism. The molecular processes responsible for generating the different gene arrangements of D. pseudoobscura is unknown, but comparative bioinformatic analyses of the D. melanogaster and D. pseudoobscura genomes as well as PCR approaches allowed us to identify inter- and intraspecific rearrangement breakpoints. The sequences of proximal and distal intraspecific breakpoints in derived and ancestral arrangements revealed a conserved motif found at high frequencies in interspecific breakpoint regions and virtually absent in coding regions. In addition, the motif is most abundant on the third chromosome when compared to other chromosomes. The motif is found in an indirect orientation in pairs of intraspecific breakpoints suggesting that genetic exchange between pairs of this conserved motif could generate paracentric inversions. If this element is responsible for genome rearrangement, then strong purifying selection appears to remove this sequence from within coding regions. Interbreakpoint matches to the conserved motif average 148 bp suggesting that selection favors accelerated divergence and degradation of the motif sequence. Further molecular experiments and bioinformatic analyses will be necessary to demonstrate a causal role for this sequence in rearranging the genome.

This work was published as part of the D. pseudoobscura genome project.