Low Amplitude Boom-and-Bust Cycles Define the Septoria Nodorum Blotch Interaction

Introduction: Septoria nodorum blotch (SNB) is a complex fungal disease of wheat caused by the Dothideomycete fungal pathogen Parastagonospora nodorum. The fungus infects through the use of necrotrophic effectors (NEs) that cause necrosis on hosts carrying matching dominant susceptibility genes. The Western Australia (WA) wheatbelt is a SNB “hot spot” and experiences significant under favorable conditions. Consequently, SNB has been a major target for breeders in WA for many years. Materials and Methods: In this study, we assembled a panel of 155 WA P. nodorum isolates collected over a 44-year period and compared them to 23 isolates from France and the USA using 28 SSR loci. Results: The WA P. nodorum population was clustered into five groups with contrasting properties. 80% of the studied isolates were assigned to two core groups found throughout the collection location and time. The other three non-core groups that encompassed transient and emergent populations were found in restricted locations and time. Changes in group genotypes occurred during periods that coincided with the mass adoption of a single or a small group of widely planted wheat cultivars. When introduced, these cultivars had high scores for SNB resistance. However, the field resistance of these new cultivars often declined over subsequent seasons prompting their replacement with new, more resistant varieties. Pathogenicity assays showed that newly emerged isolates non-core are more pathogenic than old isolates. It is likely that the non-core groups were repeatedly selected for increased virulence on the contemporary popular cultivars. Discussion: The low level of genetic diversity within the non-core groups, difference in virulence, low abundance, and restriction to limited locations suggest that these populations more vulnerable to a population crash when the cultivar was replaced by one that was genetically different and more resistant. We characterize the observed pattern as a low-amplitude boom-and-bust cycle in contrast with the classical high amplitude boom-and-bust cycles seen for biotrophic pathogens where the contrast between resistance and susceptibility is typically much greater. Implications of the results are discussed relating to breeding strategies for more sustainable SNB resistance and more generally for pathogens with NEs

Comprehensive annotation of the Parastagonospora nodorum reference genome using next-generation genomics, transcriptomics and proteogenomics

Parastagonospora nodorum, the causal agent of Septoria nodorum blotch (SNB), is an economically important pathogen of wheat (Triticum spp.), and a model for the study of necrotrophic pathology and genome evolution. The reference P. nodorum strain SN15 was the first Dothideomycete with a published genome sequence, and has been used as the basis for comparison within and between species. Here we present an updated reference genome assembly with corrections of SNP and indel errors in the underlying genome assembly from deep resequencing data as well as extensive manual annotation of gene models using transcriptomic and proteomic sources of evidence (https://github.com/robsyme/Parastagonospora_nodorum_SN15). The updated assembly and annotation includes 8,366 genes with modified protein sequence and 866 new genes. This study shows the benefits of using a wide variety of experimental methods allied to expert curation to generate a reliable set of gene models

Proportion of cysteines in <i>P</i>. <i>nodorum</i> SN15 predicted proteins before and after gene re-annotation.

<p>New proteins are more likely to be cysteine-rich. Of the 54 cysteine-rich proteins in the new annotation set (> 9% Cys by length), 16 are the products of newly annotated loci.</p

Summary of carbohydrate-active enzyme (CAZyme) family numbers in <i>P</i>. <i>nodorum</i> SN15 before and after manual re-annotation.

<p>Summary of carbohydrate-active enzyme (CAZyme) family numbers in <i>P</i>. <i>nodorum</i> SN15 before and after manual re-annotation.</p

Summary of cysteine-rich protein-products of previously unannotated genes in <i>P</i>. <i>nodorum</i> SN15.

<p>Novel cysteine-rich annotations have few BLAST hits and include potential effector candidate genes e.g. <i>SNOG_30451</i>- a degraded and truncated homolog of <i>Tox1</i>.</p

Sources of evidence used to re-annotate <i>P</i>. <i>nodorum</i> SN15 genes.

<p>This data supported 12,143 annotations with at least one source of experimental support. Additional annotations were also supported by non-experimental sources including the presence of conserved domains or homology to genes of other species.</p

Polyketide synthase genes of <i>P</i>. <i>nodorum</i> SN15.

<p>Polyketide synthase genes of <i>P</i>. <i>nodorum</i> SN15.</p

New scaffold joins improving the <i>P</i>. <i>nodorum</i> SN15 genome assembly.

<p>Joins were either predicted by mesosyntenic patterns or by terminal matches to long insert Sanger sequence reads. Orientations are indicated relative to that of scaffolds of the original assembly.</p

Summary of corrections made to the <i>P</i>. <i>nodorum</i> SN15 genome assembly.

<p>Summary of corrections made to the <i>P</i>. <i>nodorum</i> SN15 genome assembly.</p

A whole-genome dotplot of nucmer matches between scaffolds of <i>P</i>. <i>nodorum</i> and of <i>P</i>. <i>tritici-repentis</i>.

<p>The ‘dots-in-boxes’ pattern is indicative of mesosyntenic relationships between chromosomes. <i>P</i>. <i>nodorum</i> scaffolds 8 and 26 are ‘mesosyntenic’ versus <i>P</i>. <i>tritici-repentis</i> scaffold 4, as indicated by black boxes.</p