Article Figures & Data
Figures
- FIG 1
Samples included sexual and clonal populations selected for high sequence coverage. The samples were collected from throughout the world and included samples from Mexico that are sexually reproducing (green bar) as well as samples from the rest of the world that are clonally reproducing (all other bars) (2, 52). In order to attain high-quality samples from the literature and our own resequencing for the inference of copy number variation, only samples with at least 12× adjusted average read depth (AARD) were included (see Text S1 in reference 53).
- FIG 2
Strains of P. infestans show variation in gene copy number. (A) Shown are the percentage of triploid genes in sexual and clonal populations. Populations from Mexico, FAM-1, and US-22 are predominantly diploid, while populations from elsewhere in the world are predominantly triploid. (B) Bar plots of the proportion of inferred gene copy number based on allele balance over all genes for each individual. Ranking isolates from 2× to 3× show a continuous change in the proportion of gene copy number across all samples rather than discrete 2× or 3× clusters. (C) The second bar chart organizes the samples by geographic origin, starting on the left from Mexico and progressing to South America, FAM-1 (the Irish famine lineage [12]), US-1, US-8, US-11, US-18, US-22, US-23 (currently the most abundant in the United States; see Text S4 in reference 53), US-24, and finally, Europe.
- FIG 3
Gene loss in pathogenicity factors and pseudogenes occurs in individuals within populations regardless of clonal or sexual reproductive mode. The top three rows show results for individual samples, and the bottom row shows the summary for the populations sampled from Mexico (green), South America (orange), and the US-1 clonal lineage (red). Gene loss is common in individuals that may lose between 21 and 112 pathogenicity genes or pseudogenes. However, when comparing multiple samples within a population, few losses are shared. Gene loss is happening on an individual basis and is not dependent on ancestry. This pattern is observed in sexually reproducing populations (Mexico) as well as in clonally reproducing populations (South America and US-1). Gene loss is defined here as a gene from a sample with an adjusted average read depth of at least 12 and where 0 positions (base pairs) in the gene were sequenced (BOC = 0). The background for each panel is a heatmap indicating gene abundance in relation to their 5′ and 3′ intergenic spacing. Points indicate gene deletions and are colored by their functional annotation as defined in Haas et al. (23).
- FIG 4
Gene copy number variation is not restricted to a particular class of gene. The x axis shows the proportion of genes within each gene class (columns labeled at top) classified as being 2× or 3× copy number. The y axis shows the fraction of genes classified into 2× or 3× within a gene class. Columns show gene families, and rows show results by population. Isolates from Mexico (green), where P. infestans is sexually reproducing, had a gene copy number predominantly of two for all classes of genes. Isolates from South America and US-1, both considered clonally reproducing, had a gene copy number predominantly of three for all gene classes. Gene copy number varies throughout gene space and is not associated with function. Box and whisker plots summarize points that represent samples (n = 6) and the proportion of genes that were either 2× or 3× (based on the total number of 2× and 3× genes). A sample size of six was used (as in Fig. 3) to have equal samples sizes. Core, core orthologous genes; other gene families are defined as in Haas et al. (23).
- FIG 5
Gene copy number does not follow the two-speed genome hypothesis. Core orthologous genes with a copy number of three are enriched in the gene-dense (rather than gene-sparse) regions of the genome. The background for each panel is a heatmap indicating gene abundance as in Fig. 3. Orange points (with transparency) are plotted over this background, where each point is a core orthologous gene that was determined to have three copies and was positioned based on their 3′ (y axis) and 5′ (x axis) intergenic distance as in Fig. 3. Background grid and axis ticks are identical to those in Fig. 3.
- FIG 6
Ploidy variation is observed in other heterothallic Phytophthora species. Histograms showing the major and minor allele frequency observed for individuals. Samples of P. infestans are diploid or triploid. The hybrid taxon P. andina appeared predominantly diploid. Note that the y axis indicates many more heterozygous positions in these samples relative to the other species. The clade 1 species P. parasitica is diploid. However, note the “shoulder” peaks at the 3× expectation for samples P10297and P1569. The clade 2 species P. capsici demonstrated a predominance of diploidy, with the single sample Pc389 being triploid. The x axis ticks mark 0, 1/5, 1/4, 1/3, 1/2, 2/3, 3/4, 4/5, and 1 mark our expectations for pentaploid, tetraploid, triploid, and diploid. The y axis ticks in the histograms are in units of 10,000 heterozygous sites. Phylogeny adapted from Martin et al. (49). Larger histograms are presented in Text Files S6 and S7 in the supplemental material (53).
- FIG 7
Model of the genomic processes observed to date that are thought to underlie the patterns of emergence observed for clonal lineages of the Irish famine pathogen. This model proposes that sexual populations are diploid, while clonal populations are predominantly triploid. Some clones, likely rare and by chance, are clones that become dominant, displacing prior clonal lineages, as has been observed repeatedly in the United States. These dominant clones are predominantly triploid, including US-8, US-11, US-23, and the aggressive European lineage Blue13_A2 (represented in our sample by 06_3928A), while other lineages that are diploid, such as US-18 and US-22, are ephemeral or cryptic (see Text S4 in reference 53) (9). Sexual reproduction reinforces diploidy, while a triploid status might interfere with sexual reproduction but might confer fitness.
