Limits...
A genome-wide map of mitochondrial DNA recombination in yeast.

Fritsch ES, Chabbert CD, Klaus B, Steinmetz LM - Genetics (2014)

Bottom Line: Saccharomyces cerevisiae has proved to be an excellent model to dissect mitochondrial biology.Finally, to gain insights into the mechanisms involved in mitochondrial recombination, we assessed the impact of individual depletion of four genes previously associated with this process.Deletion of NTG1 and MGT1 did not substantially influence the recombination landscape, alluding to the potential presence of additional regulatory factors.

View Article: PubMed Central - PubMed

Affiliation: European Molecular Biology Laboratory, Genome Biology Unit, 69117 Heidelberg, Germany.

Show MeSH

Related in: MedlinePlus

Determination of the global and local recombination rates. (A) Determination of the global recombination rate. Each read was scanned and a genotype was assigned at each marker position. Informative DNA fragments were defined as pairs of reads overlapping at least two markers. For each of these DNA fragments, we defined a probe i of length li as the region encompassed between two consecutive markers. A given fragment can thus contain several probes as represented for probes 4 and 5. If a genotype switch occurred at the extremities of the probe, as represented for probes 2–4, we concluded that a recombination event occurred within the probe. The recombination indicator δr(i) of probe i takes the value 1 if a recombination event occurred and 0 otherwise. The global recombination rate was then calculated as the ratio of the sum of the recombination indicators and the sum of probe lengths. (B) Determination of the local recombination rate. The local recombination rate was calculated for 1-kb windows shifted by 50 bp. Similarly to the global recombination rate, we determined probes, for which the window-recombination indicator δrw(i) was estimated. For each probe, the window-recombination indicator was then defined as 0 in the absence of a recombination event or as the ratio between di, the overlap length between the probe and the window, and li, the probe length, in the case of recombination. The local recombination rate was then calculated as the sum of the recombination indicators within a given window over the total overlapping probe length.
© Copyright Policy - open-access
Related In: Results  -  Collection


getmorefigures.php?uid=PMC4196626&req=5

fig2: Determination of the global and local recombination rates. (A) Determination of the global recombination rate. Each read was scanned and a genotype was assigned at each marker position. Informative DNA fragments were defined as pairs of reads overlapping at least two markers. For each of these DNA fragments, we defined a probe i of length li as the region encompassed between two consecutive markers. A given fragment can thus contain several probes as represented for probes 4 and 5. If a genotype switch occurred at the extremities of the probe, as represented for probes 2–4, we concluded that a recombination event occurred within the probe. The recombination indicator δr(i) of probe i takes the value 1 if a recombination event occurred and 0 otherwise. The global recombination rate was then calculated as the ratio of the sum of the recombination indicators and the sum of probe lengths. (B) Determination of the local recombination rate. The local recombination rate was calculated for 1-kb windows shifted by 50 bp. Similarly to the global recombination rate, we determined probes, for which the window-recombination indicator δrw(i) was estimated. For each probe, the window-recombination indicator was then defined as 0 in the absence of a recombination event or as the ratio between di, the overlap length between the probe and the window, and li, the probe length, in the case of recombination. The local recombination rate was then calculated as the sum of the recombination indicators within a given window over the total overlapping probe length.

Mentions: We identified single-nucleotide polymorphisms (SNPs) and small structural variants (SVs) in a genome-wide fashion, using the Unified Genotyper variant caller from GATK (McKenna et al. 2010). The vcf files obtained as output were then filtered out to keep only the SNPs and SVs that exhibited a coverage of >100×. In addition, for the parental genomes only the variants with an allele frequency of 1 were kept, as these strains are clonal and haploid and should therefore have only one single genotype for a given position. These SNPs and SVs are referred to as markers in the following sections (Figure 2).


A genome-wide map of mitochondrial DNA recombination in yeast.

Fritsch ES, Chabbert CD, Klaus B, Steinmetz LM - Genetics (2014)

Determination of the global and local recombination rates. (A) Determination of the global recombination rate. Each read was scanned and a genotype was assigned at each marker position. Informative DNA fragments were defined as pairs of reads overlapping at least two markers. For each of these DNA fragments, we defined a probe i of length li as the region encompassed between two consecutive markers. A given fragment can thus contain several probes as represented for probes 4 and 5. If a genotype switch occurred at the extremities of the probe, as represented for probes 2–4, we concluded that a recombination event occurred within the probe. The recombination indicator δr(i) of probe i takes the value 1 if a recombination event occurred and 0 otherwise. The global recombination rate was then calculated as the ratio of the sum of the recombination indicators and the sum of probe lengths. (B) Determination of the local recombination rate. The local recombination rate was calculated for 1-kb windows shifted by 50 bp. Similarly to the global recombination rate, we determined probes, for which the window-recombination indicator δrw(i) was estimated. For each probe, the window-recombination indicator was then defined as 0 in the absence of a recombination event or as the ratio between di, the overlap length between the probe and the window, and li, the probe length, in the case of recombination. The local recombination rate was then calculated as the sum of the recombination indicators within a given window over the total overlapping probe length.
© Copyright Policy - open-access
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC4196626&req=5

fig2: Determination of the global and local recombination rates. (A) Determination of the global recombination rate. Each read was scanned and a genotype was assigned at each marker position. Informative DNA fragments were defined as pairs of reads overlapping at least two markers. For each of these DNA fragments, we defined a probe i of length li as the region encompassed between two consecutive markers. A given fragment can thus contain several probes as represented for probes 4 and 5. If a genotype switch occurred at the extremities of the probe, as represented for probes 2–4, we concluded that a recombination event occurred within the probe. The recombination indicator δr(i) of probe i takes the value 1 if a recombination event occurred and 0 otherwise. The global recombination rate was then calculated as the ratio of the sum of the recombination indicators and the sum of probe lengths. (B) Determination of the local recombination rate. The local recombination rate was calculated for 1-kb windows shifted by 50 bp. Similarly to the global recombination rate, we determined probes, for which the window-recombination indicator δrw(i) was estimated. For each probe, the window-recombination indicator was then defined as 0 in the absence of a recombination event or as the ratio between di, the overlap length between the probe and the window, and li, the probe length, in the case of recombination. The local recombination rate was then calculated as the sum of the recombination indicators within a given window over the total overlapping probe length.
Mentions: We identified single-nucleotide polymorphisms (SNPs) and small structural variants (SVs) in a genome-wide fashion, using the Unified Genotyper variant caller from GATK (McKenna et al. 2010). The vcf files obtained as output were then filtered out to keep only the SNPs and SVs that exhibited a coverage of >100×. In addition, for the parental genomes only the variants with an allele frequency of 1 were kept, as these strains are clonal and haploid and should therefore have only one single genotype for a given position. These SNPs and SVs are referred to as markers in the following sections (Figure 2).

Bottom Line: Saccharomyces cerevisiae has proved to be an excellent model to dissect mitochondrial biology.Finally, to gain insights into the mechanisms involved in mitochondrial recombination, we assessed the impact of individual depletion of four genes previously associated with this process.Deletion of NTG1 and MGT1 did not substantially influence the recombination landscape, alluding to the potential presence of additional regulatory factors.

View Article: PubMed Central - PubMed

Affiliation: European Molecular Biology Laboratory, Genome Biology Unit, 69117 Heidelberg, Germany.

Show MeSH
Related in: MedlinePlus