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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.

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Related in: MedlinePlus

Detailed characterization of the TS15.1 region.(A) aCGH data for all tetrads across chromosome XV. The area within the red box contains TS15.1, and is shown in more detail in panel B, (B) Raw aCGH data and (C) inferred duplications (yellow) and deletions (blue).
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pgen-1000502-g004: Detailed characterization of the TS15.1 region.(A) aCGH data for all tetrads across chromosome XV. The area within the red box contains TS15.1, and is shown in more detail in panel B, (B) Raw aCGH data and (C) inferred duplications (yellow) and deletions (blue).

Mentions: We sought to determine the endpoints of TS15.1, the largest of the six segments, more precisely by manual inspection of the hybridization data (Figure 4). The segment was initially identified by eleven closely linked Class 3 regions, including 12–17, 19, 20, and 22–24. Probes 18 and 21 had been excluded from consideration initially because they were not present on the particular batch of microarrays we used.


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)

Detailed characterization of the TS15.1 region.(A) aCGH data for all tetrads across chromosome XV. The area within the red box contains TS15.1, and is shown in more detail in panel B, (B) Raw aCGH data and (C) inferred duplications (yellow) and deletions (blue).
© Copyright Policy
Related In: Results  -  Collection

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

pgen-1000502-g004: Detailed characterization of the TS15.1 region.(A) aCGH data for all tetrads across chromosome XV. The area within the red box contains TS15.1, and is shown in more detail in panel B, (B) Raw aCGH data and (C) inferred duplications (yellow) and deletions (blue).
Mentions: We sought to determine the endpoints of TS15.1, the largest of the six segments, more precisely by manual inspection of the hybridization data (Figure 4). The segment was initially identified by eleven closely linked Class 3 regions, including 12–17, 19, 20, and 22–24. Probes 18 and 21 had been excluded from consideration initially because they were not present on the particular batch of microarrays we used.

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