, Volume 136, Issue 1, pp 5–11

Sequence signatures of a recent chromosomal rearrangement in Drosophila mojavensis


DOI: 10.1007/s10709-008-9296-0

Cite this article as:
Runcie, D.E. & Noor, M.A.F. Genetica (2009) 136: 5. doi:10.1007/s10709-008-9296-0


The X-chromosome inversion, Xe, distinguishes Drosophila mojavensis and D. arizonae. Earlier work mapped the breakpoints of this inversion to large intervals and provided hypotheses for the locations of the breakpoints within 3000-bp intergenic regions on the D. mojavensis genome sequence assembly. Here, we sequenced these regions directly in the putatively ancestral D. arizonae X-chromosome. We find that the two inversion breakpoints are near an inverted gene duplication and a common repetitive element, respectively, and these features were likely present in the non-inverted ancestral chromosome on the D. mojavensis lineage. Contrary to an earlier hypothesis, the inverted gene duplication appears to predate the inversion. We find no sequence similarity between the breakpoint regions in the D. mojavensis ancestor, excluding an ectopic-exchange model of chromosome rearrangements. We also found no evidence that staggered single-strand breaks caused the inversion. We suggest these features may have contributed to the chromosomal breakages resulting in this inversion.


Chromosomal inversionGene duplicationGenome evolutionTransposable element





Thousand basepairs


Nonsynonymous substitution rate


Synonymous substitution rate

Supplementary material

10709_2008_9296_MOESM2_ESM.eps (5.3 mb)
Supplementary Fig. 1 Amino acid alignment of CG2056 in D. mojavnsis, D. arizonae and D. virilis. Amino acids selected for dn/ds-based sequence conservation analysis are highlighted in light orange (EPS 5411 kb)

Copyright information

© Springer Science+Business Media B.V. 2008

Authors and Affiliations

  1. 1.Biology Department, Biological SciencesDuke UniversityDurhamUSA