Repeat-induced point mutations driving Parastagonospora nodorum genomic diversity are balanced by selection against non-synonymous mutations

Abstract

Parastagonospora nodorum is necrotrophic fungal pathogen of wheat with significant genomic resources. Population-level pangenome data for 173 isolates, of which 156 were from Western Australia (WA) and 17 were international, were examined for overall genomic diversity and effector gene content. A heterothallic core population occurred across all regions of WA, with asexually-reproducing clonal clusters in dryer northern regions. High potential for SNP diversity in the form of repeat-induced point mutation (RIP)-like transitions, was observed across the genome, suggesting widespread 'RIP-leakage' from transposon-rich repetitive sequences into non-repetitive regions. The strong potential for RIP-like mutations was balanced by negative selection against non-synonymous SNPs, that was observed within protein-coding regions. Protein isoform profiles of known effector loci (SnToxA, SnTox1, SnTox3, SnTox267, and SnTox5) indicated low-levels of non-synonymous and high-levels of silent RIP-like mutations. Effector predictions identified 186 candidate secreted predicted effector proteins (CSEPs), 69 of which had functional annotations and included confirmed effectors. Pangenome-based effector isoform profiles across WA were distinct from global isolates and were conserved relative to population structure, and may enable new approaches for monitoring crop disease pathotypes.

Fig. 1

Locations across Western Australia (dark grey) where Parastagonospora nodorum isolates were sourced for whole-genome sequencing.

Fig. 2. Summary of mutation across the Parastagonospora nodorum pangenome, relative to the Sn15 reference isolate.

Rings proceeding inwards represent: Sn15 chromosomes from 1 to 23 (black/grey, accessory chromosome = red), with labels indicating the locations of 4 effector loci present in Sn15; G:C content (grey); gene density (green); Predector (effector-likelihood) score (green/red); repetitive DNA density (red); composite RIP index (CRI) (green/red); SNP site density (blue = total, yellow = (RIP-like) transition mutations, red=non-synonymous RIP-like transitions; presence-absence variation (PAV) relative to all isolates (red). The geographic region, predicted phylogeny, and population grouping of isolates are indicated alongside corresponding PAV tracks.

Fig. 3. Summary of SNP mutation sites (left) detected across the Parastagonospora nodorum pangenome relative to the Sn15 reference isolate.

SNP mutation sites were categorised (middle) into RIP-like (C↔T or A↔G SNPs) and Other/non-RIP-like (not C↔T or A↔G SNPs) and by their predicted effects on protein-coding genes (right).

Fig. 4. Structure and pathogenicity features of the Western Australian (WA) Parastagonospora nodorum population.

SNP-derived phylogeny (left) of Western Australian and internationally-sampled P. nodorum isolates (see legend), shows: isolates (branch labels); sampling year; sub-population groups (green) from this study (right) and a previous study (left); mating-type loci (blue); and the presence of effector loci (red-middle) and effector protein isoforms (red-right, from left-to-right: highest to lowest frequency). An alternate version with overlaid branch lengths is presented in Supplementary Fig. 1.