DOI: 10.6084/m9.figshare.13325915.v1
title: P. nodorum WA pangenome: supplementary material

description: Supplementary material for the manuscript: "Novel effector candidates and large accessory genome revealed by population-level pan-genomic analysis of <i>Parastagonospora nodorum</i>"<br>These captions are summarised, for full captions please see the paper.<br><br><b>Figure 1:</b> The structure and features of the Western Australian (WA) <i>Parastagonospora nodorum</i> population.<br><b>Figure 2</b>: A circos plot showing SNP density over each of the 23 chromosomes in the SN15 genome assembly.<br><br><b>Figure 3.</b> A circos plot showing the proportion of RIP-like (CA↔TA or TG↔TA) mutations over transition (C↔T or G↔A) mutations for each of the 23 chromosomes in the SN15 genome assembly.<br><br><b>Figure 4.</b> A circos plot showing each <i>Parastagonospora nodorum</i> genome assembly alignment coverage for each of the 23 chromosomes in <i>P. nodorum</i> SN15.<br><br><b>Figure 5.</b> Dispensable and multi-copy orthogroups for each isolate in the <i>P. nodorum</i> pan-genome.<br><br><b>Supp. table 1.</b>Additional published genomes used in this study.<br><b>Supp. table 2.</b>Summary of Illumina sequencing read contamination detection.<br><b>Supp. table 3.</b>Parameters used to filter short variants by quality, and statistics of variants in the filtered set.<br><b>Supp. table 4.</b>Population diversity statistics and results of STRUCTURE analysis.<br><b>Supp. table 5.</b>Genome assembly for all isolates sequenced in this study. Statistics were collected using BBtools stats and QUAST.<br><b>Supp. table 6.</b>Summaries statistics of transposable elements, rRNA and tRNA genes, and repeat annotations for each assembled genome.<br><b>Supp. table 7.</b>Summary statistics of gene predictions for each isolate. Numbers are provided for each prediction method.<br><b>Supp. table 8.</b>SNP, counts RIP-like SNP ratios, and genome assembly alignment coverage data used to plot circular heatmaps in figures 2, 3, and 4.<br><b>Supp. table 9.</b>Orthogroup counts for each isolate used to plot figure 5.<br><b>Supp. table 10.</b><br>Functional annotation, selection, presence absence data for each orthogroup. A single representative sequence for each orthogroup was selected as the member with the highest Predector score. The full orthogroup annotation can be found at https://doi.org/10.6084/m9.figshare.12966971.v1 .<br><b>Supp. table 11.</b><br>GO term and effector enrichment tests for predicted functions and groups of orthogroups.<br><b>Supp. data 1.</b>MultiQC reports of read trimming and quality control for Illumina sequencing reads.<br><b>Supp. data 2.</b>Boxplots showing short variant (SNP, insertion/deletion, Mixed) genotype quality (GQ) statistics for each isolate. Each chromosome in SN15 is shown on a separate page in the PDF.<b><br></b><b>Supp. data 3.</b><br>Violin plots showing short variant (SNP, insertion/deletion, Mixed) genotype read depth (DP) statistics for each isolate. Each chromosome in SN15 is shown on a separate page in the PDF.<b><br></b><b>Supp. data 4.</b><br>Bar plots showing amounts of missing short variant genotype information for each isolate. Each chromosome in SN15 is shown on a separate page in the PDF.<br><b>Supp. data 5.</b>SNP locus quality statistics visualised for each chromosome in SN15 on separate pages in the PDF.<br><b>Supp. data 6.</b>Insertion and Deletion (INDEL) locus quality statistics visualised for each chromosome in SN15 on separate pages in the PDF.<br><b>Supp. data 7.</b>Mixed variant (multi-nucleotide variations, or insertions/deletions with SNPs at the same locus) locus quality statistics visualised for each chromosome in SN15 on separate pages in the PDF.<br><b>Supp. data 8.</b>Kernel density estimate plots showing the distributions of short variant locus quality statistics.<br><b>Supp. data 9.</b>Maximum likelihood phylogenetic tree estimated from 45,194 SNPs using IQTree. The file is in Newick format. Clade confidence values show SH-aLRT and UFBoot support separated by ‘/’.<br><b>Supp. data 10.</b>MSA and trees of ToxA, 1, 3 CDS/codon-aligned regions from pan-genome, to support prevalence of RIP-like SNPs across pan-genome in confirmed effector loci<br><b>Supp. data 11.</b>Example dot plot alignments between scaffolds and chromosomes containing orthogroups in PAV clusters selected from figure 5.<b><br></b><b>Supp. data 12.</b><br>Phylogenetic tree estimated using ASTRAL, combining gene trees computed using FastTree from all single copy orthogroups.<br><b>Supp. figure 1.</b><br>Phylogeographic representation of the WA <i>P. nodorum</i> populations, with phylogeny generated from whole-genome SNP data relative to alignment to the SN15 reference genome, and yellow lines indicating the approximate location of sampling.<br><b>Supp. figure 2.</b><br>Tanglegram comparison of predicted SNP phylogeny with the SSR predicted tree from Phan et al. (2020).<br><b>Supp. figure 3.</b>Comparison of population cluster assignment between this study and as identified by Phan et al. (2020).<br><b>Supp. figure 4.</b>Numbers of isolates in clusters from each sampling location.<br><b>Supp. figure 5.</b><br>Numbers of isolates in clusters from each sampling year.<br><b>Supp. figure 6.</b>The first six principal components computed from bi-allelic SNP data plotted for each sampling location.<b><br></b><b>Supp. figure 7.</b><br>The first six principal components computed from bi-allelic SNP data plotted against each sampling year.<br><b>Supp. figure 8.</b>Multi-gene tree computed by ASTRAL from all single copy orthogroups, compared with the tree predicted using SNP data.<br><b>Supp. figure 9.</b>Multi-gene tree computed by ASTRAL from all single copy orthogroups, compared with the tree predicted using SSR data presented by Phan et al. (2020).<br><b>Supp. figure 10.</b>Plots showing relationship between RIP-like mutations and selection or effector predictions. RIP proportion shows the proportion of RIP-like mutations in a window of within 1 kb of the representative member of an orthogroup in SN15. The RIP proportion was compared with the overall dN/dS ratio for each orthogroup (A), the dN/dS ratio within the orthogroup for clade with the highest dN/dS ratio (B), the rank of Predector scores with lower ranks being more likely to be effectors (C), and the Predector scores themselves (D) where higher scores suggest effector candidacy. No association was observed between any of these features and RIP proportions.