Isolation and analysis of the breakpoint sequences of chromosome inversion In(3L)Payne in Drosophila melanogaster.

Abstract

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 that the sequence features associated with inversion breakpoints would reveal much about the mutational origin, uniqueness, and genealogical history of individual inversion polymorphisms, but the cloning of breakpoint sequences is not trivial. With the aid of a method for rapid recovery of DNA clones sanning rearrangement breakpoints, we recover and examine the DNA sequences spanning the breakpoints of the cosmopolitan inversionln(3L)Payne in Drosophila melanogaster. By examining the sequence diversity associated with six standard and seven inverted chromosomes from natural populations, we find that the inversion is monophyletic in origin, the sequences are genetically isolated from recombination at the breakpoints, and there is no association with features such as transposable elements. The inverted sequences show 17-fold less nucleotide polymorphism, but there are eight fixed differences in the region spnning both breakpoints. This suggests that this inversion is not recently derived. Finally, Northern analysis and transcript mapping find that the distal breakpoint has disrupted three transcripts that are normally expressed in the standard arrangement. Incidentally, the method introduced here can be used to isolate breakpoint sequences of arrangements associated with many human diseases.Chromosomal inversions were first discovered by Sturtevant in 1917 as recombination modifiers in Drosophila melanogaster (1), and the subsequent study of chromosomal rearrangements in Drosophila became important in evolutionary biology and population genetics (2, 3). Nevertheless, after decades of study, a number of questions and assumptions about inversions have persisted. For instance, inversions are assumed to be mutationally unique (i.e., monophyletic in origin); however, it is now known that transposable elements exhibit genomic site preferences, can generate rearrangements, and therefore are potential causal agents of chromosomal inversions in natural populations (4-6). It has also been proposed that inversions persist in natural populations as recombination-protected coadapted gene complexes (3), but the possibility that mutations unique to the inversion event are involved in early establishment has not been addressed. These and other questions can be addressed by molecular analysis of chromosomal breakpoint sequences.The historical cosegregation of large segments of associated chromosomal arms with inversions (by suppression of products of recombination in heterokaryotypes) is not absolute at the population level but is expected to decrease with distance from the inversion breakpoints, where recombination is most suppressed. Taken PCRs. Nonspecific PCR. Amplifications were done as described (7) with the following modifications. Native Taq polymerase (Perkin-Elmer/Cetus) was treated in a solution of DNase I...

Chromosome Inversions, Local Adaptation and Speciation

“…The break in the chromosome may result in a fortuitous selective advantage, either by disrupting a gene where the breakpoint occurs or by changing gene expression in the chromosomal neighborhood. This kind of ''position effect'' has been documented in the inversion In(3L)Payne in Drosophila (Wesley and Eanes 1994). On the other hand, the results from searches for gene disruption caused by the inversions that distinguish humans and chimps have to date been negative (Kehrer-Sawatzki et al 2002, 2005.…”

“…It is thus plausible that the inversion affects patterns of gene expression, a result known from other inversions (Wesley and Eanes 1994). A survey of polymorphism in the vicinity of the breakpoint shows a pattern reminiscent of Adh: it appears that one or more sites have been under balancing selection for much longer than the age of the inversion and further that haplotype frequencies vary geographically (Andolfatto and Kreitman 2000).…”

Chromosomal Rearrangement Inferred From Comparisons of 12 Drosophila Genomes

“…The transposable-element model proposed that these repetitive sequences act as sites for ectopic exchange within chromosomal arms, leading to rearrangement. Sequences at inversion breakpoints have (Mathiopoulos and Lanzaro 1995;Mathiopoulos et al 1998Mathiopoulos et al , 1999Cáceres et al 1999Cáceres et al , 2001) and have not found repetitive sequences at the breakpoints of gene arrangements (Wesley and Eanes 1994;Andolfatto and Kreitman 2000;Anderson et al 2005;Matzkin et al 2005). Several studies of rearrangement breakpoints have shown that the gene duplications often accompany the rearrangement event (Matzkin et al 2005;Ranz et al 2007).…”

A molecular perspective on a complex polymorphic inversion system with cytological evidence of multiply reused breakpoints

“…Indeed, extant sequences of polymorphic inversion breakpoints are expected to better reflect the sequences in the original inverted chromosome. Despite the extensive knowledge accumulated on inversion polymorphism in Drosophila, there are relatively few polymorphic inversion breakpoints molecularly characterized both in any particular species and across species (but see Wesley and Eanes, 1994;Andolfatto et al, 1999;Cáceres et al, 1999;Casals et al, 2003;Matzkin et al, 2005;Richards et al, 2005;Delprat et al, 2009;Papaceit et al, 2013;Puerma et al, 2014). The number of molecularly characterized breakpoints drops even more when inversions with cytological evidence of reused breakpoints are considered Puerma et al, 2014).…”