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Nucleic Acids Research Advance Access published online on August 26, 2009
Nucleic Acids Research, doi:10.1093/nar/gkp650
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© The Author 2009. Published by Oxford University Press.
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

Yeast genome analysis identifies chromosomal translocation, gene conversion events and several sites of Ty element insertion

Yoshiyuki Shibata, Ankit Malhotra, Stefan Bekiranov and Anindya Dutta*

Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA 22908, USA

*To whom correspondence should be addressed. Tel: +1 (434) 924 1227; Fax: +1 (434) 924 5069; Email: ad8q{at}virginia.edu

Received April 3, 2009. Revised July 20, 2009. Accepted July 20, 2009.

Paired end mapping of chromosomal fragments has been used in human cells to identify numerous structural variations in chromosomes of individuals and of cancer cell lines; however, the molecular, biological and bioinformatics methods for this technology are still in development. Here, we present a parallel bioinformatics approach to analyze chromosomal paired-end tag (ChromPET) sequence data and demonstrate its application in identifying gene rearrangements in the model organism Saccharomyces cerevisiae. We detected several expected events, including a chromosomal rearrangement of the nonessential arm of chromosome V induced by selective pressure, rearrangements introduced during strain construction and gene conversion at the MAT locus. In addition, we discovered several unannotated Ty element insertions that are present in the reference yeast strain, but not in the reference genome sequence, suggesting a few revisions are necessary in the latter. These data demonstrate that application of the chromPET technique to a genetically tractable organism like yeast provides an easy screen for studying the mechanisms of chromosomal rearrangements during the propagation of a species.


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