DOI: 10.6084/m9.figshare.13325915.v3
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 based on membership in reference genomes (preferentially SN15 &gt; SN2000 &gt; SN4 &gt; SN79 &gt; any other isolate), then by minimum distance to median length within the orthogroup, breaking ties randomly. The full orthogroup annotation can be found at https://doi.org/10.6084/m9.figshare.12966971.v4.<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.<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.