title: Yeast genome analysis identifies chromosomal translocation, gene conversion events and several sites of Ty element insertion.
abstract: 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.
authors.affiliation: Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA 22908, USA.
authors.forename: Yoshiyuki
authors.initials: Y
authors.lastname: Shibata
authors.forename: Ankit
authors.initials: A
authors.lastname: Malhotra
authors.forename: Stefan
authors.initials: S
authors.lastname: Bekiranov
authors.forename: Anindya
authors.initials: A
authors.lastname: Dutta
mesh_terms: D026923:Amino Acid Transport Systems, Basic / Q000235:genetics; D015825:Chromosomes, Fungal; D004251:DNA Transposable Elements; D005785:Gene Conversion; D005800:Genes, Fungal; D008040:Genetic Linkage; D016681:Genome, Fungal; D015698:Genomic Library; D023281:Genomics / Q000379:methods*; D012441:Saccharomyces cerevisiae / Q000235:genetics*; D029701:Saccharomyces cerevisiae Proteins / Q000235:genetics; D014178:Translocation, Genetic
chemical_list: D026923:Amino Acid Transport Systems, Basic; C502212:CAN1 protein, S cerevisiae; D004251:DNA Transposable Elements; D029701:Saccharomyces cerevisiae Proteins