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Gene Finding on the Y: Fruitful Strategy in Drosophila does not Deliver in Anopheles

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Abstract

The Anopheles gambiae genome project yielded almost complete sequences for the autosomes and for a large part of the X chromosome, however, no information for the Y chromosome was obtained. Yet, by design, fragmented Y chromosome sequences should be present in the resulting assembly. Here we report the search for Anopheles Y chromosome genes using a strategy successfully applied for identification of Y genes in Drosophila. A complete set of the unmapped scaffolds was targeted in a broad TBLASTN search using both A. gambiae predicted genes and all proteins from nr database as query sequences. After filtering of the BLAST report, we selected 181 scaffolds possibly containing fragments of Y chromosome genes to experimentally test their Y-linkage. Surprisingly, none of the tested sequences appeared to originate from the Y chromosome. Several factors could account for the failure to detect Y genes, including their different organization in A. gambiae compared to Drosophila and the suboptimal quality of the assembly and annotation of the Anopheles genome. Regardless of the cause, our results illuminate problems associated with the genome analysis of outbred organisms.

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Authors and Affiliations

  1. Center for Tropical Disease Research and Training, Department of Biology, University of Notre Dame, 46556, Notre Dame, Indiana, USA

    Jaroslaw Krzywinski, Mathew A. Chrystal & Nora J. Besansky

  2. Department of Biology, University of Texas at Arlington, 76019-0498, Arlington, Texas, USA

    Jaroslaw Krzywinski

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  1. Jaroslaw Krzywinski
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  2. Mathew A. Chrystal
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  3. Nora J. Besansky
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Correspondence to Nora J. Besansky.

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Krzywinski, J., Chrystal, M.A. & Besansky, N.J. Gene Finding on the Y: Fruitful Strategy in Drosophila does not Deliver in Anopheles. Genetica 126, 369–375 (2006). https://doi.org/10.1007/s10709-005-1985-3

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  • DOI: https://doi.org/10.1007/s10709-005-1985-3

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