Abstract
Inversion polymorphisms have occupied a privileged place in Drosophila genetic research since their discovery in the 1920s.
Indeed, inversions seem to be nearly ubiquitous, and the majority of species that have been thoroughly surveyed have been found to
be polymorphic for one or more chromosomal inversions. Despite enduring interest, however, inversions remain difficult to study
because their effects are often cryptic, and few efficient assays have been developed. Even in Drosophila melanogaster, in which
inversions can be reliably detected and have received considerable attention, the breakpoints of only three inversions have been
characterized molecularly. Hence, inversion detection and assay design remain important unsolved problems. Here, we present
a method for identification and local de novo assembly of inversion breakpoints using next-generation paired-end reads derived from
D. melanogaster isofemale lines. PCR and cytological confirmations demonstrate that our method can reliably assemble inversion
breakpoints, providing tools for future research on D. melanogaster inversions as well as a framework for detection and assay design of
inversions and other chromosome aberrations in diverse taxa.
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