Emergence and diversification of a highly invasive chestnut pathogen lineage across southeastern Europe
- Swiss Federal Institute for Forest, Snow and Landscape Research (WSL), Switzerland
- Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuchâtel, Switzerland
- Plant Pathology, Institute of Integrative Biology, ETH Zürich, Switzerland
Figures
Figure 1 with 2 supplements
Genome-wide analyses of global Cryphonectria parasitica isolates.
(A) Map of global sampling locations and (B) principal component analysis (PCA) of the 230 sequenced C. parasitica isolates. Colors indicate PCA clusters (CL1–CL4) and are as in (A). (C) SplitsTree …
Figure 1—figure supplement 1
Genome-wide association mapping (GWAS) outcome for the mating type (MAT) locus.
The red line shows the p-value-based threshold to exclude MAT-locus-associated single nucleotide polymorphisms (SNPs) for population structure analyses.
Figure 1—figure supplement 2
Distribution of observed single nucleotide polymorphism (SNP) filtration quality values.
Figure 2
Demographic models for global Cryphonectria parasitica populations.
Constant, expansion, bottleneck, bottleneck-expansion, and bottlegrowth population models were tested for three clusters (i.e., European/North American CL1, mixed European/Asian CL2, and Asian CL3 …
Figure 3 with 2 supplements
Phylogenetic network structure of the main European/North American subgroup and spatial distribution of S12 across Europe.
(A) The highlighted branches represent the most abundant vegetative compatibility types. Isolates belonging to the S12 outbreak lineage (EU-12; mating type MAT-1, n = 105) are marked with a red …
Figure 3—figure supplement 1
SplitsTree of all non-S12 isolates showing full isolate identifiers.
Isolates identified as S12 are listed in Supplementary file 1.
Figure 3—figure supplement 2
Per site population recombination rate ρ of European/North American Cryphonectria parasitica populations as inferred with LDhat.
Figure 4 with 2 supplements
Analysis of donors to the S12 lineage genotypes.
Averaged coancestry matrix and population tree of the North American/European subgroup estimated by fineSTRUCTURE. The heatmap indicates averaged coancestry between populations. Populations sharing …
Figure 4—figure supplement 1
fineSTRUCTURE convergence plots.
(A) FineSTRUCTURE Markov Chain–Monte Carlo (MCMC) traces. (B) Pairwise coincidence matrix of population assignments.
Figure 4—figure supplement 2
Full averaged coancestry matrix showing isolate identifiers.
Figure 5 with 3 supplements
Transposable element (TE) landscape and copy number variation.
(A) Genome-wide coverage of transposable elements (in 10 kb windows) matched by with normalized read depth for the S12 and non-S12 lineages (North America and Europe only). vic loci: vegetative …
Figure 5—figure supplement 1
Genetic diversity within the S12 lineage.
Minor allele frequency distribution spectrum for three classes of variants. The number of polymorphic positions was normalized to the total number of polymorphic positions in S12 and non-S12 …
Figure 5—figure supplement 2
Pairwise genome-wide nucleotide differences between S12 and non-S12 isolates.
Figure 5—figure supplement 3
Normalized read depth distribution across C. parasitica isolates.
Figure 6
Polymorphism segregating in the S12 lineage.
(A) Alternative allele frequencies spectra across the genome for the S12 lineage (n = 105) compared to all other analyzed European (non-S12; n = 92). (B) Genome-wide nucleotide diversity (Pi) for …
Figure 7
Fine-scale genetic diversity analyses of the S12 lineage.
(A) SplitsTree and (B) principal component analysis (PCA) of the S12 mating type MAT-1 outbreak isolates (n = 105). Symbols and colors are as in (A). (C) Scheme of successful mating pairs of S12 …
Additional files
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Supplementary file 1
Information on all analyzed isolates including sampling location, vegetative compatibility type (EU-type), (SSR) simple sequence repeats genotyping outcome, collector information, collection years, and NCBI accessions.
- https://cdn.elifesciences.org/articles/56279/elife-56279-supp1-v1.xlsx
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Supplementary file 2
Initial and best-fit parameters as well as likelihoods and Akaike information criterion (AIC) values as inferred by dadi for demographic analyses.
Cluster names correspond to clusters as shown in Figure 1A.
- https://cdn.elifesciences.org/articles/56279/elife-56279-supp2-v1.xlsx
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Supplementary file 3
List of the genes in regions with signatures of recent positive selection (based on RAiSD).
Putative functions are shown by (PFAM) Protein families (database) and Gene Ontology (GO) annotations. Single nucleotide polymorphisms (SNPs) and the corresponding composite μ statistic are shown.
- https://cdn.elifesciences.org/articles/56279/elife-56279-supp3-v1.xlsx
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Supplementary file 4
Summary of MAT-1 and MAT-2 isolate pairings used for testing sexual recombination in S12 populations.
*Isolates from the S12 MAT-1 lineage.
- https://cdn.elifesciences.org/articles/56279/elife-56279-supp4-v1.xlsx
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Transparent reporting form
- https://cdn.elifesciences.org/articles/56279/elife-56279-transrepform-v1.pdf
