Limits...
Systematic identification of balanced transposition polymorphisms in Saccharomyces cerevisiae.

Faddah DA, Ganko EW, McCoach C, Pickrell JK, Hanlon SE, Mann FG, Mieczkowska JO, Jones CD, Lieb JD, Vision TJ - PLoS Genet. (2009)

Bottom Line: High-throughput techniques for detecting DNA polymorphisms generally do not identify changes in which the genomic position of a sequence, but not its copy number, varies among individuals.The presence of low-copy repetitive sequences at the junctions of this segment suggests that it may have arisen through ectopic recombination.Our methodology and findings provide a starting point for exploring the origins, phenotypic consequences, and evolutionary fate of this largely unexplored form of genomic polymorphism.

View Article: PubMed Central - PubMed

Affiliation: Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.

ABSTRACT
High-throughput techniques for detecting DNA polymorphisms generally do not identify changes in which the genomic position of a sequence, but not its copy number, varies among individuals. To explore such balanced structural polymorphisms, we used array-based Comparative Genomic Hybridization (aCGH) to conduct a genome-wide screen for single-copy genomic segments that occupy different genomic positions in the standard laboratory strain of Saccharomyces cerevisiae (S90) and a polymorphic wild isolate (Y101) through analysis of six tetrads from a cross of these two strains. Paired-end high-throughput sequencing of Y101 validated four of the predicted rearrangements. The transposed segments contained one to four annotated genes each, yet crosses between S90 and Y101 yielded mostly viable tetrads. The longest segment comprised 13.5 kb near the telomere of chromosome XV in the S288C reference strain and Southern blotting confirmed its predicted location on chromosome IX in Y101. Interestingly, inter-locus crossover events between copies of this segment occurred at a detectable rate. The presence of low-copy repetitive sequences at the junctions of this segment suggests that it may have arisen through ectopic recombination. Our methodology and findings provide a starting point for exploring the origins, phenotypic consequences, and evolutionary fate of this largely unexplored form of genomic polymorphism.

Show MeSH

Related in: MedlinePlus

Segregation in a cross between strains carrying a transposed segment.In this example, two haploid parental strains harbor a particular genomic region (black) on different chromosomes. Crossing the parents leads to a diploid that contains two copies of the transposed segment. Sporulation leads to either a tetratype (TT) pattern (one duplication and one deletion); a non-parental ditype (NPD) pattern (two duplications and two deletions), or a parental ditype (PD) pattern (neither duplications nor deletions). The relative frequencies depend on the position of the transposed segment relative to the centromeres in each parent.
© Copyright Policy
Related In: Results  -  Collection


getmorefigures.php?uid=PMC2682701&req=5

pgen-1000502-g001: Segregation in a cross between strains carrying a transposed segment.In this example, two haploid parental strains harbor a particular genomic region (black) on different chromosomes. Crossing the parents leads to a diploid that contains two copies of the transposed segment. Sporulation leads to either a tetratype (TT) pattern (one duplication and one deletion); a non-parental ditype (NPD) pattern (two duplications and two deletions), or a parental ditype (PD) pattern (neither duplications nor deletions). The relative frequencies depend on the position of the transposed segment relative to the centromeres in each parent.

Mentions: Here, we demonstrate an experimental methodology for identifying balanced structural polymorphisms genome-wide at kilobase resolution. It is based on the observation that if a given segment of DNA resides on different chromosomes in a diploid, random assortment of chromosomes during meiosis will cause that segment to appear as a duplication or deletion among a fraction of the resulting haploids (Figure 1). Thus, one can identify such unlinked transposed segments (TS) by using array-based Comparative Genomic Hybridization (aCGH) [6] to measure the copy number of small genomic intervals in the two haploid parents of a diploid, and in the haploid products of diploid meiosis.


Systematic identification of balanced transposition polymorphisms in Saccharomyces cerevisiae.

Faddah DA, Ganko EW, McCoach C, Pickrell JK, Hanlon SE, Mann FG, Mieczkowska JO, Jones CD, Lieb JD, Vision TJ - PLoS Genet. (2009)

Segregation in a cross between strains carrying a transposed segment.In this example, two haploid parental strains harbor a particular genomic region (black) on different chromosomes. Crossing the parents leads to a diploid that contains two copies of the transposed segment. Sporulation leads to either a tetratype (TT) pattern (one duplication and one deletion); a non-parental ditype (NPD) pattern (two duplications and two deletions), or a parental ditype (PD) pattern (neither duplications nor deletions). The relative frequencies depend on the position of the transposed segment relative to the centromeres in each parent.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC2682701&req=5

pgen-1000502-g001: Segregation in a cross between strains carrying a transposed segment.In this example, two haploid parental strains harbor a particular genomic region (black) on different chromosomes. Crossing the parents leads to a diploid that contains two copies of the transposed segment. Sporulation leads to either a tetratype (TT) pattern (one duplication and one deletion); a non-parental ditype (NPD) pattern (two duplications and two deletions), or a parental ditype (PD) pattern (neither duplications nor deletions). The relative frequencies depend on the position of the transposed segment relative to the centromeres in each parent.
Mentions: Here, we demonstrate an experimental methodology for identifying balanced structural polymorphisms genome-wide at kilobase resolution. It is based on the observation that if a given segment of DNA resides on different chromosomes in a diploid, random assortment of chromosomes during meiosis will cause that segment to appear as a duplication or deletion among a fraction of the resulting haploids (Figure 1). Thus, one can identify such unlinked transposed segments (TS) by using array-based Comparative Genomic Hybridization (aCGH) [6] to measure the copy number of small genomic intervals in the two haploid parents of a diploid, and in the haploid products of diploid meiosis.

Bottom Line: High-throughput techniques for detecting DNA polymorphisms generally do not identify changes in which the genomic position of a sequence, but not its copy number, varies among individuals.The presence of low-copy repetitive sequences at the junctions of this segment suggests that it may have arisen through ectopic recombination.Our methodology and findings provide a starting point for exploring the origins, phenotypic consequences, and evolutionary fate of this largely unexplored form of genomic polymorphism.

View Article: PubMed Central - PubMed

Affiliation: Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.

ABSTRACT
High-throughput techniques for detecting DNA polymorphisms generally do not identify changes in which the genomic position of a sequence, but not its copy number, varies among individuals. To explore such balanced structural polymorphisms, we used array-based Comparative Genomic Hybridization (aCGH) to conduct a genome-wide screen for single-copy genomic segments that occupy different genomic positions in the standard laboratory strain of Saccharomyces cerevisiae (S90) and a polymorphic wild isolate (Y101) through analysis of six tetrads from a cross of these two strains. Paired-end high-throughput sequencing of Y101 validated four of the predicted rearrangements. The transposed segments contained one to four annotated genes each, yet crosses between S90 and Y101 yielded mostly viable tetrads. The longest segment comprised 13.5 kb near the telomere of chromosome XV in the S288C reference strain and Southern blotting confirmed its predicted location on chromosome IX in Y101. Interestingly, inter-locus crossover events between copies of this segment occurred at a detectable rate. The presence of low-copy repetitive sequences at the junctions of this segment suggests that it may have arisen through ectopic recombination. Our methodology and findings provide a starting point for exploring the origins, phenotypic consequences, and evolutionary fate of this largely unexplored form of genomic polymorphism.

Show MeSH
Related in: MedlinePlus