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Originally published as Genetics Published Articles Ahead of Print on March 21, 2005.
Genetics, Vol. 170, 1143-1152, July 2005, Copyright © 2005
doi:10.1534/genetics.104.038810
The Structure and Population Genetics of the Breakpoints Associated With the Cosmopolitan Chromosomal Inversion In(3R)Payne in Drosophila melanogaster
Luciano M. Matzkin1,2, Thomas J. S. Merritt2, Chen-Tseh Zhu and Walter F. Eanes3
Department of Ecology and Evolution, Stony Brook University, Stony Brook, New York 11794
3 Corresponding author: Department of Ecology and Evolution, Stony Brook University, Stony Brook, NY 11794.
E-mail: walter{at}life.bio.sunysb.edu
We report here the breakpoint structure and sequences of the Drosophila melanogaster cosmopolitan chromosomal inversion In(3R)P. Combining in situ hybridization to polytene chromosomes and long-range PCR, we have identified and sequenced the distal and proximal breakpoints. The breakpoints are not simple cut-and-paste structures; gene fragments and small duplications of DNA are associated with both breaks. The distal breakpoint breaks the tolkin (tok) gene and the proximal breakpoint breaks CG31279 and the tolloid (tld) gene. Functional copies of all three genes are found at the opposite breakpoints. We sequenced a representative sample of standard (St) and In(3R)P karyotypes for a 2-kb portion of the tok gene, as well as the same 2 kb from the pseudogene tok fragment found at the distal breakpoint of In(3R)P chromosomes. The tok gene in St arrangements possesses levels of polymorphism typical of D. melanogaster genes. The functional tok gene associated with In(3R)P shows little polymorphism. Numerous single-base changes, as well as deletions and duplications, are associated with the truncated copy of tok. The overall pattern of polymorphism is consistent with a recent origin of In(3R)P, on the order of Ne generations. The identification of these breakpoint sequences permits a simple PCR-based screen for In(3R)P.
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