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. 2019 Feb 26;8:e43606. doi: 10.7554/eLife.43606

Figure 4. Preferential sharing of alleles near immunity genes.

(A) Enrichment of tsCgCrSNPs and non-synonymous tsCgCrSNPs for genes associated with significant GO terms (means, blue; medians, red). Each point represents values calculated for an individual gene. For example, in the upper subplot each point is the number of tsSNPs identified in a gene divided by the total number of SNPs identified for a gene. GO terms with a significantly increased ratio of nonsynonymous changes are highlighted with a yellow box. (B) tsCgCrSNP frequency as a function of distance to the closest NLR cluster. (C) Pairwise genetic diversity at neutral (four-fold degenerate) sites as a function of distance to the closest NLR cluster. For (B–C) the thick black lines are mean values calculated in 500 bp windows as a function of distance from a NLR gene. The thin black lines are mean values from 100 random gene sets of equivalent size. The grey polygons are the range of values across all 100 random gene sets. (D) Chromosomal locations of Bal regions with the strongest evidence for balancing selection. Immunity genes with known function in A. thaliana in each region indicated. (E) Values for Watterson’s estimator (Θw) of diversity in Bal regions, calculated from 20 kb windows. (F) Tajima’s D. Dots in (E, F) are a random sample of 1000 windows for non candidate windows. Boxplots report the median 1st and 3rd quantiles of all windows in each class. (G) An example of the site level (dots) and windowed (green) decrease in Fst at the first region on chromosome 2. The subregion without data near 1 Mb is a CC-NLR cluster, which was largely masked for variant calling.

Figure 4—source data 1. Regions with evidence for balancing selection.
elife-43606-fig4-data1.xlsx (12KB, xlsx)
DOI: 10.7554/eLife.43606.025
Figure 4—source data 2. Spearman’s correlations of allele frequencies for different classes of tsSNPs.
Only SNPs with a minor allele frequency greater than 0.05 in all three populations were considered.
elife-43606-fig4-data2.xlsx (45.4KB, xlsx)
DOI: 10.7554/eLife.43606.026

Figure 4.

Figure 4—figure supplement 1. Quality metrics for ssSNPs and tsSNPs in C. rubella.

Figure 4—figure supplement 1.

(A–D) Average coverage and concordance for reference calls (A and C) or non-reference calls (B and D). ssSNPs or tsSNPs outside of regions with significant evidence for balancing selection (red and blue) or inside of these regions (green and purple). Concordance describes the fraction of reads covering a position that supports a particular allele. For example a heterozygous site might have A in 50% of the reads and T in 50% of the reads. The concordance at this site would be 0.5. We show this statistic because our SNP calling method favors homozygous calls in the selfing lineages. If we are missing some heterozygous sites, this would be revealed in the concordance values.
Figure 4—figure supplement 2. Analysis of IBS in balanced regions and genome-wide.

Figure 4—figure supplement 2.

(A) The relationship between genome-wide and balanced region IBS. Dark blue, west population accessions, Light blue, east population accessions. (B) The decay of IBS genome-wide (red) and within balanced regions (blue) as a function of distance from the centre of C. grandiflora’s range. (C) The genome-wide distribution of IBD segment lengths.