Abstract
The malaria vector Anopheles gambiae maintains high levels of inversion polymorphism that facilitate its exploitation of diverse ecological settings across tropical Africa. Molecular characterization of inversion breakpoints is a first step toward understanding the processes that generate and maintain inversions. Here we focused on inversion 2Rj because of its association with the assortatively mating Bamako chromosomal form of An. gambiae, whose distinctive breeding sites are rock pools beside the Niger River in Mali and Guinea. Sequence and computational analysis of 2Rj revealed the same 14.6 kb insertion between both breakpoints, which occurred near but not within predicted genes. Each insertion consists of 5.3 kb terminal inverted repeat arms separated by a 4 kb spacer. The insertions lack coding capacity, and are comprised of degraded remnants of repetitive sequences including class I and II transposable elements. Because of their large size and patchwork composition, and as no other instances of these insertions were identified in the An. gambiae genome, they do not appear to be transposable elements. The 14.6 kb modules inserted at both 2Rj breakpoint junctions represent low copy repeats (LCRs, also called segmental duplications) that are strongly implicated in the recent (∼0.4Ne generations) origin of 2Rj. The LCRs contribute to further genome instability, as demonstrated by an imprecise excision event at the proximal breakpoint of 2Rj in field isolates.
Highlights
Seventy years ago, Dobzhansky expressed ‘‘...little doubt that chromosomal changes are one of the mainsprings of evolution’’ [1]
From a BAC library prepared from pairwise alignment of 2R+j standard (PEST) [27], candidate clones known to map in the vicinity of the 2R+j proximal breakpoint were hybridized to 2Rj chromosomes from the BKO strain of the Bamako chromosomal form of An. gambiae
Each low-copy repeats (LCRs) is bounded by identical 5.3 kb inverted repeats (IRs) separated by a 4 kb spacer
Summary
Dobzhansky expressed ‘‘...little doubt that chromosomal changes are one of the mainsprings of evolution’’ [1] This view was founded on evidence from Drosophila in which rearrangements of the banding pattern are readily detected on giant (polytene) chromosomes, the widespread occurrence of chromosomal rearrangements is apparent in light of the many whole genome sequences from yeasts to humans and plants. Adaptations associated with alternative arrangements can be preserved, despite migration and gene flow between their carriers, through suppressed recombination in inversion heterozygotes. This mechanism may contribute to ongoing ecotypic differentiation and speciation [5,6], explaining why fixed chromosomal inversion differences often distinguish closely related species [4]
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