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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

Comparative genomic evidence that S288C harbors the ancestral form of TS15.1.Annotated genes (open boxed arrows) are shown for S. paradoxus and S. bayanus contigs relative to the known structure of the region in S288C and the inferred structure in Y101. S. paradoxus contig 539 matches the gene order of S288C across the proximal endpoint of TS15.1 while S. bayanus contig 223 matches the gene order of S288C across the distal endpoint. The green bar shows the position of the gap on chromosome XV of Y101. Each scalebar tick represents 1 kilobase.
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pgen-1000502-g008: Comparative genomic evidence that S288C harbors the ancestral form of TS15.1.Annotated genes (open boxed arrows) are shown for S. paradoxus and S. bayanus contigs relative to the known structure of the region in S288C and the inferred structure in Y101. S. paradoxus contig 539 matches the gene order of S288C across the proximal endpoint of TS15.1 while S. bayanus contig 223 matches the gene order of S288C across the distal endpoint. The green bar shows the position of the gap on chromosome XV of Y101. Each scalebar tick represents 1 kilobase.

Mentions: To determine the ancestral state for TS15.1, we examined the genome sequence of S. paradoxus and S. bayanus [24],[40]. In the initial genome assembly, S. paradoxus “contig 539” contains homologs to the genes YOL157C (probe 25), YOL156W (probe 27) and YOL155C (probe 30), which span the proximal endpoint of the transposed segment and are arranged in the same order and orientation as in S288C (Figure 8). Likewise, S. bayanus contig 223 contains homologs to the genes YOL163W (probe 10), YOL162W (probe 11) and YOL161C (probe 13) which span the distal endpoint of the transposed segment are also arranged in the same order and orientation (Figure 8). While it is not possible to compare the genome organization distal to the transposed segment due to the incompleteness and fragmentation of the assemblies in this region for S. paradoxus and S. bayanus, this nonetheless strongly suggests that TS15.1S288C is the ancestral state.


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)

Comparative genomic evidence that S288C harbors the ancestral form of TS15.1.Annotated genes (open boxed arrows) are shown for S. paradoxus and S. bayanus contigs relative to the known structure of the region in S288C and the inferred structure in Y101. S. paradoxus contig 539 matches the gene order of S288C across the proximal endpoint of TS15.1 while S. bayanus contig 223 matches the gene order of S288C across the distal endpoint. The green bar shows the position of the gap on chromosome XV of Y101. Each scalebar tick represents 1 kilobase.
© Copyright Policy
Related In: Results  -  Collection

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

pgen-1000502-g008: Comparative genomic evidence that S288C harbors the ancestral form of TS15.1.Annotated genes (open boxed arrows) are shown for S. paradoxus and S. bayanus contigs relative to the known structure of the region in S288C and the inferred structure in Y101. S. paradoxus contig 539 matches the gene order of S288C across the proximal endpoint of TS15.1 while S. bayanus contig 223 matches the gene order of S288C across the distal endpoint. The green bar shows the position of the gap on chromosome XV of Y101. Each scalebar tick represents 1 kilobase.
Mentions: To determine the ancestral state for TS15.1, we examined the genome sequence of S. paradoxus and S. bayanus [24],[40]. In the initial genome assembly, S. paradoxus “contig 539” contains homologs to the genes YOL157C (probe 25), YOL156W (probe 27) and YOL155C (probe 30), which span the proximal endpoint of the transposed segment and are arranged in the same order and orientation as in S288C (Figure 8). Likewise, S. bayanus contig 223 contains homologs to the genes YOL163W (probe 10), YOL162W (probe 11) and YOL161C (probe 13) which span the distal endpoint of the transposed segment are also arranged in the same order and orientation (Figure 8). While it is not possible to compare the genome organization distal to the transposed segment due to the incompleteness and fragmentation of the assemblies in this region for S. paradoxus and S. bayanus, this nonetheless strongly suggests that TS15.1S288C is the ancestral state.

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