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Sequence signatures of a recent chromosomal rearrangement in Drosophila mojavensis

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Abstract

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.

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Abbreviations

bp:

Basepair

kb:

Thousand basepairs

dn:

Nonsynonymous substitution rate

ds:

Synonymous substitution rate

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Acknowledgements

The authors would like to thank A. Chang for providing Drosophila mojavensis flies for these analyses, A. Chang, W. Etges, and three anonymous reviewers for helpful comments on the manuscript, and A. Somerville for technical assistance. Funding was provided by NSF grants 0509780 and 0715484 and NIH grant GM076051.

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Correspondence to Mohamed A. F. Noor.

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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)

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Runcie, D.E., Noor, M.A.F. Sequence signatures of a recent chromosomal rearrangement in Drosophila mojavensis . Genetica 136, 5–11 (2009). https://doi.org/10.1007/s10709-008-9296-0

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  • DOI: https://doi.org/10.1007/s10709-008-9296-0

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