ISOLATION AND ANALYSIS OF THE BREAKPOINT SEQUENCES OF CHROMOSOME INVERSION IN(3L)PAYNE IN DROSOPHILA-MELANOGASTER

Chromosomal rearrangements constitute a significant feature of genome evolution, and inversion polymorphisms in Drosophila have been studied intensely for decades. Population geneticists have long recognized th at the sequence features associated with inversion breakpoints would r eveal much about the mutational origin, uniqueness, and genealogical h istory of individual inversion polymorphisms, but the cloning of break point sequences is not trivial. With the aid of a method for rapid rec overy of DNA clones spanning rearrangement breakpoints, we recover and examine the DNA sequences spanning the breakpoints of the cosmopolita n inversion In(3L)Payne in Drosophila melanogaster. By examining the s equence diversity associated with six standard and seven inverted chro mosomes from natural populations, we find that the inversion is monoph yletic in origin, the sequences are genetically isolated from recombin ation at the breakpoints, and there is no association with features su ch as transposable elements. The inverted sequences show 17-fold less nucleotide polymorphism, but there are eight fixed differences in the region spanning both breakpoints. This suggests that this inversion is not recently derived. Finally, Northern analysis and transcript mappi ng find that the distal breakpoint has disrupted three transcripts tha t are normally expressed in the standard arrangement. Incidentally, th e method introduced here can be used to isolate breakpoint sequences o f arrangements associated with many human diseases.