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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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Results of PCR assays for the boundaries of TS15.1 in tetrad 27.Based on the aCGH data, deletion of TS15.1 was expected in spore 27A. Probes tested in all six tetrads are indicated by asterisks. Due to the repetitive nature of subtelomeric segments 0–10, PCR assays produced ambiguous results (marked as “not determined”). See also Table S3.
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pgen-1000502-g005: Results of PCR assays for the boundaries of TS15.1 in tetrad 27.Based on the aCGH data, deletion of TS15.1 was expected in spore 27A. Probes tested in all six tetrads are indicated by asterisks. Due to the repetitive nature of subtelomeric segments 0–10, PCR assays produced ambiguous results (marked as “not determined”). See also Table S3.

Mentions: Initially, we tested primer pairs corresponding to probes 11 through 32 and probe 36 in the two parental strains, the reference strain, and the four spores from tetrad 27 (Figure 5, Tables S2 and S3). Amplification was obtained from all genotypes using primer pairs from probes 11, 26–30, 32, and 36. Primers corresponding to probes 13 through 25 failed to amplify products only in spore 27A, consistent with the hypothesis that this spore did not inherit TS15.1 from either parent. Probes 12 and 31 failed to amplify in spore 27A and D, and also in Y101, indicating that segments 12 and 31 are candidate endpoints for TS15.1. To map the right endpoint more finely, we designed new primers to split probe 31 into two halves, 31L and 31R. The results support 31L as being external to the transposed segment, and identify 31R as containing the endpoint (as illustrated in Figure 6).


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)

Results of PCR assays for the boundaries of TS15.1 in tetrad 27.Based on the aCGH data, deletion of TS15.1 was expected in spore 27A. Probes tested in all six tetrads are indicated by asterisks. Due to the repetitive nature of subtelomeric segments 0–10, PCR assays produced ambiguous results (marked as “not determined”). See also Table S3.
© Copyright Policy
Related In: Results  -  Collection

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

pgen-1000502-g005: Results of PCR assays for the boundaries of TS15.1 in tetrad 27.Based on the aCGH data, deletion of TS15.1 was expected in spore 27A. Probes tested in all six tetrads are indicated by asterisks. Due to the repetitive nature of subtelomeric segments 0–10, PCR assays produced ambiguous results (marked as “not determined”). See also Table S3.
Mentions: Initially, we tested primer pairs corresponding to probes 11 through 32 and probe 36 in the two parental strains, the reference strain, and the four spores from tetrad 27 (Figure 5, Tables S2 and S3). Amplification was obtained from all genotypes using primer pairs from probes 11, 26–30, 32, and 36. Primers corresponding to probes 13 through 25 failed to amplify products only in spore 27A, consistent with the hypothesis that this spore did not inherit TS15.1 from either parent. Probes 12 and 31 failed to amplify in spore 27A and D, and also in Y101, indicating that segments 12 and 31 are candidate endpoints for TS15.1. To map the right endpoint more finely, we designed new primers to split probe 31 into two halves, 31L and 31R. The results support 31L as being external to the transposed segment, and identify 31R as containing the endpoint (as illustrated in Figure 6).

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