Segmental Duplication, Microinversion, and Gene Loss Associated with a Complex Inversion Breakpoint Region in Drosophila

Abstract

Chromosomal inversions are usually portrayed as simple two-breakpoint rearrangements changing gene order but not gene number or structure. However, increasing evidence suggests that inversion breakpoints may often have a complex structure and entail gene duplications with potential functional consequences. Here, we used a combination of different techniques to investigate the breakpoint structure and the functional consequences of a complex rearrangement fixed in Drosophila buzzatii and comprising two tandemly arranged inversions sharing the middle breakpoint: 2m and 2n. By comparing the sequence in the breakpoint regions between D. buzzatii (inverted chromosome) and D. mojavensis (noninverted chromosome), we corroborate the breakpoint reuse at the molecular level and infer that inversion 2m was associated with a duplication of a ~13 kb segment and likely generated by staggered breaks plus repair by nonhomologous end joining. The duplicated segment contained the gene CG4673, involved in nuclear transport, and its two nested genes CG5071 and CG5079. Interestingly, we found that other than the inversion and the associated duplication, both breakpoints suffered additional rearrangements, that is, the proximal breakpoint experienced a microinversion event associated at both ends with a 121-bp long duplication that contains a promoter. As a consequence of all these different rearrangements, CG5079 has been lost from the genome, CG5071 is now a single copy nonnested gene, and CG4673 has a transcript ~9 kb shorter and seems to have acquired a more complex gene regulation. Our results illustrate the complex effects of chromosomal rearrangements and highlight the need of complementing genomic approaches with detailed sequence-level and functional analyses of breakpoint regions if we are to fully understand genome structure, function, and evolutionary dynamics.

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

“…The recent detection, also through genome sequence comparison, of inverted duplications at the breakpoints of 5 out of the 8 studied inversions segregating in natural populations of D. melanogaster (Corbett-Detig et al, 2012) would support the Ranz et al (2007) proposal for the melanogaster species group. This proportion does not seem, however, to hold for the repleta group of species, neither for fixed inversions-with inverted duplications in 3 out of 10 fixed inversions (Calvete et al, 2012;Guillén and Ruiz, 2012)-nor for polymorphic inversions in D. buzzatii, where the generating mechanism of the three characterized inversions was ectopic recombination between transposable elements (Cáceres et al, 1999;Casals et al, 2003;Delprat et al, 2009).…”

Drosophila Chromosomal Polymorphism: From Population Aspects to Origin Mechanisms of Inversions

“…Inversions 2m and 2n 2m inversion with 13 Kbp duplications in both breakpoints; origin of the inversion by staggered breaks [60] …”

“…Although the reuse intra or interspecific of the inversions breakpoints, at cytological level, is common and well documented in the Drosophila genus, the characterization at DNA sequence level is still limited [59][60][61]. In silico comparisons of total genomes of different species available [62], estimate between 1.5 [63] and 2.27 [64] times the reuse of breakpoints throughout the evolutionary history of the species of this genus.…”

“…The physically close breaks in the chromosome cause failures in the correct pairing of the nitrogen bases, and the chromosomal regions separate. The inversion is due to the junction of the 5′ end with the 3′ end of the other breakpoint [60,70]. Duplicated DNA segments and in opposite orientations (delimiting the inverted chromosome segment) are the result of the repair and the main recognition mark of this mechanism [59].…”

“…There are also analyses of fixed inversions 2m and 2n in D. buzzatti, which are distributed in tandem and share the central breakpoint at the cytological level [60]. The delimitation and molecular characterization of the breakpoints were based on the genomic library of bacterial artificial chromosomes (BACs), and physical map of this species [102], and in the genome of the related species Drosophila mojavensis Patterson, 1940 [62], which did not exhibit such inversions.…”