Genome-wide survey of post-meiotic segregation during yeast recombination
- Equal contributors
1 European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
2 European Molecular Biology Laboratory, European Bioinformatics Institute, Cambridge CB10 1SD, UK
3 Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080-4990, USA
Genome Biology 2011, 12:R36 doi:10.1186/gb-2011-12-4-r36Published: 11 April 2011
Additional file 1:
Markers where post-meiotic segregation has been inferred. The first_S288c and last_S288c columns correspond to the chromosomal coordinates of the marker using the S288c coordinate system. The rest of the headers give the spore number, the chromosome (chr), the S288c:YJM789 segregation ratio and the S288c and YJM789 genotype of the marker.
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Additional file 2:
Marker coordinates and genotype calls for all spores. The first, last and chr columns are as described in the legend of Additional file 1. The type column contains S for SNPs, I for insertions, D for deletions, and M for probe sets that interrogated more than one polymorphism (that is, consecutive SNPs, or a SNP near an insertion or deletion). Apart from those columns there is one column per genotyped cell, the header of which is composed of "wt", the tetrad number (1, 5, 7, 8), the mother or daughter cell (1,2) and the spore (a, b, c, d), each separated by an underscore. A genotype call of 1 corresponds to S288c.
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Additional file 3:
Inferred CO and NCO interval locations. The first_S288c and last_S288c columns correspond to the maximal method described in , in which the tract is defined by the two nearest unconverted markers. In the type column, × denotes a CO and C denotes an NCO as described in . The pms column denotes whether a PMS event was observed in a given recombination interval. Other column headers give tetrad number and spore letter.
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Additional file 4:
Supplementary figures. Figure S1: position of PMS markers within recombination tracts. Each row corresponds to a single recombination event and each vertical segment depicts a marker involved in such an event. Markers where PMS occurred are shown as larger red segments. Indel markers are shown as rectangles instead of segments. Vertical axis labels give tetrad, chromosome, and first base of the recombination event. For the event wt_7 chr06:74792, also depicted in Figure 2b, only one conversion tract is shown. Figure S2: PMS tends to occur at the ends of conversion tracts. The figure shows the degree to which there is overrepresentation of events with PMS markers exactly at one end or the other of the conversion tract. In 1,000 simulations, the fraction of recombination events with one or more terminal PMS markers was recorded (see Materials and methods). The histogram shows the distribution of these fractions; the blue vertical line shows the observed fraction of events with terminal PMS events. Figure S3: Events where more than one PMS marker was observed. Four recombination events had more than one marker where PMS occurred. Two of these events are depicted in Figure 2 in the main text and the other two are illustrated here: (a) a CO in chromosome II; and (b) a NCO in chromosome IX. As in Figure 2, red/blue vertical segments represent markers with the S288c/YJM789 genotype along the chromosomes of the two mother and daughter cells resulting from the first mitosis of each spore (A, B, C and D). Horizontal black lines indicate inferred NCOs, and the diagonal, inferred COs. Green vertical segments immediately on top of the coordinate axis denote markers where PMS occurred and orange segments denote markers with non-Mendelian segregation. Figure S4: SNP distribution along gene conversion tracts. For each recombination interval, markers were assigned to the fraction of the interval they spanned. For example, in a one-marker interval, the one and only marker was assigned to the full range from 0% to 100%; for a three marker interval, the first marker was assigned to 0% to 33%, the second to 33% to 66%, and the third to 66% to 100%, and so on. Non-SNP markers were ignored. The frequency with which any position corresponded to a particular SNP type was then computed over the full range of 0% to 100%. No SNP type appears to show positional bias.
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