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Nucleic Acids Research Advance Access originally published online on February 23, 2009
Nucleic Acids Research 2009 37(7):2264-2273; doi:10.1093/nar/gkp085
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Nucleic Acids Research, 2009, Vol. 37, No. 7 2264-2273
© 2009 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Genomics

Novel sequencing strategy for repetitive DNA in a Drosophila BAC clone reveals that the centromeric region of the Y chromosome evolved from a telomere{dagger}

María Méndez-Lago1,2, Jadwiga Wild2, Siobhan L. Whitehead3, Alan Tracey3, Beatriz de Pablos1, Jane Rogers3, Waclaw Szybalski2,* and Alfredo Villasante1,*

1Centro de Biología Molecular ‘Severo Ochoa’ (CSIC-UAM), Cantoblanco, 28049 Madrid, Spain 2McArdle Laboratory for Cancer Research, University of Wisconsin Medical School, Madison, WI 53706-1599, USA and 3The Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, CB10 1SA, UK

*To whom correspondence should be addressed. Tel: +34 91 1964682; Fax: +34 91 1964420; Email: avillasante{at}cbm.uam.es Correspondence may also be addressed to Waclaw Szybalski. Tel: +1 608 262 1259; Fax: +1 608 2622824; Email: szybalski{at}oncology.wisc.edu

Received November 12, 2008. Revised January 29, 2009. Accepted January 30, 2009.

The centromeric and telomeric heterochromatin of eukaryotic chromosomes is mainly composed of middle-repetitive elements, such as transposable elements and tandemly repeated DNA sequences. Because of this repetitive nature, Whole Genome Shotgun Projects have failed in sequencing these regions. We describe a novel kind of transposon-based approach for sequencing highly repetitive DNA sequences in BAC clones. The key to this strategy relies on physical mapping the precise position of the transposon insertion, which enables the correct assembly of the repeated DNA. We have applied this strategy to a clone from the centromeric region of the Y chromosome of Drosophila melanogaster. The analysis of the complete sequence of this clone has allowed us to prove that this centromeric region evolved from a telomere, possibly after a pericentric inversion of an ancestral telocentric chromosome. Our results confirm that the use of transposon-mediated sequencing, including positional mapping information, improves current finishing strategies. The strategy we describe could be a universal approach to resolving the heterochromatic regions of eukaryotic genomes.

{dagger}The GenBank accession numbers for the sequences reported in this article are CU076040 [GenBank] and FM992409.


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