Supplemental material for Winzeler et al., 2003. Genetics Vol 163

 

Genetic Diversity in Yeast Assessed with Whole-Genome Oligonucleotide Arrays

Elizabeth A. Winzeler(1,3,5), Cristian I. Castillo-Davis(2), Guy Oshiro(1), David Liang(1), Daniel R. Richards(4), Yingyao Zhou(1), and Daniel L. Hartl(2)

 

  1. Genomics Institute of the Novartis Research Foundation
    10675 John Jay Hopkins
    San Diego, California 92121

    2.
  2. Department of Organismic and Evolutionary Biology
    Harvard University
    Cambridge, Massachusetts 02138

    3.
  3. Current Address:
    The Scripps Research Institute
    Department of Cell Biology
    10550 Torrey Pines Rd.
    La Jolla, California 92037

    4.
  4. Department of Genetics
    Stanford University School of Medicine
    Stanford, California 95307

    5.
  5. Correspondence should be addressed to E.A. Winzeler.

Tables

Sequencing results

List of SFPs found in the project (tab separated text)

Files

Affymetrix CEL files

Figures

Supplemental Figure 2a

Supplemental Figure 2b

Supplemental Figure 2c

Supplemental Figure 5

Supplemental Figure 2A. Distribution of variation for 13 strains for 4 chromosomes. The position of every unique probe is shown at the bottom of each chromosome group and the locations of allelic variation for 13 strains is shown above. In addition, genomic regions that are likely to be inherited from an S288C-like strain are highlighted in gray for EM93, W303, A364, 99R, and S1278b (Determined as described in Materials and Methods). Though sequencing showed a very low frequency of false positives, false negatives were found. This is a result of the stringency associated with the prediction routine. On average, chromosome I showed the most variability with 1.5 polymorphic probes per every 1000 bases of sequence. Chromosome III, which is very also small, exhibited the lowest density of polymorphic probes (less than 0.5 per 1000). Thus chromosome size may have little to do with the frequency of polymorphic probes and the high numbers of polymorphic probes for chromosome I may be that the source of chromosome I in the reference strain, X2180-1A, is different than from its other chromosomes, especially as X2180-1A is not a wild isolate. In this respect, obtaining the genome sequence of one or more true natural isolates of S. cerevisiae would be informative.

Supplemental Figure 2B.

Supplemental Figure 2C.

Supplement Figure 5. Histogram showing base position relative to the ends of the 25mer probe of polymorphisms detected by sequencing (PCR products, or whole regions of the genome) within the oligonucleotide probe.