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Additional file 1: Fig. S1. Distribution of minor allele frequency (MAF) of SNP loci detected in limber pine resistant gene analogs (RGAs). Fig. S2. SNP frequencies of limber pine resistance gene analogs (RGAs). Fig. S3. Sequencing depth of SNP loci in individual samples. The percentages of total SNPs (x-axis) have a coverage of a certain depth (y-axis). SNP depth was assessed in each individual of seed family LJ-112. The plot displays data for SNPs (967) with MAF ≥ 0.3 and about 70% of them have a minimum depth at 10 x in all samples except one. Fig. S4. The extent of missing data for 967 SNP loci in 96 individual samples of seed family LJ-112. Individual samples with missing data were calculated as a percentage of the total (y-axis) and plotted across the cumulative total SNPs (x-axis). Over 80% of total SNPs showed missing data in less than 10% of total individual samples. Fig. S5. Correlation of SNP positions of the same NLR gene mapped on the same linkage groups (LGs) by both Fluidigm amplicon-bases targeted-seq (TS) and whole exome-seq (WES). (a) Comparison of TS and WES in seed family LJ-112; (b) comparison of TS and WES between seed families LJ-112 and PHA-106. Fig. S6. Physical distances (bp) of paired SNPs mapped by Fluidigm amplicon-bases targeted-seq (TS) and whole exome-seq (WES). Fig. S7. Identification of NLR alleles significantly associated with MGR-conferred phenotypes using extreme-phenotype genome-wide association study (XP-GWAS). (a) Quantile–quantile plot of the test statistic: 5608 SNPs detected in 354 RGAs with coverage > 50 were subjected to association analysis. (b) Manhattan plot: top SNPs were selected for each genes and plotted against genetic maps of 12 linkage groups, and those genes not mapped so far were included as a separate group. Significant threshold value (p = 1.69 × 10− 4) is presented by a horizontal dash line.

Additional file 4: Figure S4. Pearson correlation analysis of viral RNA levels as measured by RNA-seq analysis and qRT-PCR.

Additional file 1: Figure S1. Phylogenetic trees of the family Totiviridae based on the deduced amino acid sequences of capsid proteins. Sequences were aligned using Clustal Omega, and trees were generated using the maximum likelihood method with a bootstrap test of 100 iterations in MEGA 6 software. (a) Totiviruses grouping in the genus Totivirus. (b) Toti-like sequences potentially belonging to other genera of the family Totiviridae. Sequence identifications are the same as shown in Fig. 2.

Additional file 2: Figure S2. Pearson correlation analysis of fungal virulence and viral RNA levels of CrTV4 as detected by qRT-PCR. Cronartium ribicola vcr2 samples were set at a virulence level of 1 (N = 6) and avcr2 samples were set at a virulence level of 0 (N = 27).

Additional file 3: Figure S3. CrTV4 RNA levels measured by qRT-PCR in 33 Cronartium ribicola samples. Bars show average RNA levels of each virus with standard error of the mean (SEM). One-way Analysis of Variance (ANOVA) showed significant difference among seven types of samples (Pâ =â 0.014).

Comparisons of orders of Pinus conserved genes between P. flexilis Cr4 linkage group (LG) and LG8 of P. taeda consensus maps. P. taeda LG-8 was revised based on mapping data reported by Westbrook et al. [30]. (PPTX 328Â kb)

Functional classification of the Cronartium ribicola reference transcriptome assembled de novo from RNA-seq data based on gene ontology (GO). Subcategories of biological process, molecular function, and cellular component are indicated as: GO:0008152, metabolic process; GO:0009987, cellular process; GO:0044699, single-organism process; GO:0050896, response to stimulus; GO:0051179, localization; GO:0065007, biological regulation; GO:0071840, cellular component organization or biogenesis; GO:0032502, developmental process; GO:0023052, signaling; GO:0032501, multicellular organismal process; GO:0000003, reproduction; GO:0040007, growth; GO:0051704, multi-organism process; GO:0040011, locomotion; GO:0002376, immune system process; GO:0022610, biological adhesion; GO:0048511, rhythmic process; GO:0001906, cell killing; GO:0005488, binding; GO:0003824, catalytic activity; GO:0005198, structural molecule activity; GO:0005215, transporter activity; GO:0009055, electron carrier activity; GO:0001071, nucleic acid binding transcription factor activity; GO:0016209, antioxidant activity; GO:0030234, enzyme regulator activity; GO:0060089, molecular transducer activity; GO:0000988, protein binding transcription factor activity; GO:0004872, receptor activity; GO:0045735, nutrient reservoir activity; GO:0016530, metallochaperone activity; GO:0005623, cell; GO:0043226, organelle; GO:0032991, macromolecular complex; GO:0016020, membrane; GO:0031974, membrane-enclosed lumen; GO:0005576, extracellular region; GO:0009295, nucleoid; GO:0030054, cell junction; GO:0045202, synapse; GO:0031012, extracellular matrix; GO:0055044, symplast. (PPTX 104 kb)

Statistical characteristics of de-novo assembly of Cronartium ribicola transcriptomes. Table S2. Open reading frames (ORFs) predicted by TransDecoder for the Cri proteome. Table S3. BLAST analysis of Cronartium ribicola transcript and protein sequences against other databases. Table S4. Annotation and classification of Cronartium ribicola carbohydrate-active enzymes. Table S5. Classification of Cronartium ribicola transporter proteins. Table S6. HMM domain identification of Cronartium ribicola secreted proteins. Table S7. Cronartium ribicola candidate effectors with annotation of Pfam domains and putative functions in pathogenicity. Table S8. Expression data (FPKM) of the Cronartium ribicola reference transcriptome based on RNA-seq analysis. Table S9. Annotated Cronartium ribicola genes with opposite expression patterns between cankered stems and infected Ribes leaves at urediniospore stage. Table S10. qRT-PCR primers for analysis of Cronartium ribicola genes. Table S11. Evaluation of transcript expression level by qRT-PCR. Gene expression level was calculated as relative quantification (RQ) using ABI ExpressionSuite software. Table S12. Gene ontology (GO) enrichment analysis of differentially expressed genes (DEGs). Table S13. Gene ontology (GO) analysis of differentially expressed genes (DEGs) up-regulated in urediniospores relative to aeciospores. Table S14. BLAST and GO analyses of differentially expressed genes (DEGs) up-related in early compatible WPBR interactions relative to incompatible WPBR interactions. (PPTX 2770 kb)

Top-hit species distribution for the Cronartium ribicola transcripts measured by BLASTx analysis using the BLAST2GO program. (PPTX 143 kb)