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Local adaptation drives the diversification of effectors in the fungal wheat pathogen Parastagonospora nodorum in the United States

By Jonathan K. Richards, Eva H Stukenbrock, Jessica Carpenter, Zhaohui Liu, Christina Cowger, Justin D. Faris, Timothy Friesen

Posted 31 May 2019
bioRxiv DOI: 10.1101/657007 (published DOI: 10.1371/journal.pgen.1008223)

Filamentous fungi rapidly evolve in response to environmental selection pressures, exemplified by their genomic plasticity. Parastagonospora nodorum, a fungal pathogen of wheat and causal agent of septoria nodorum blotch, responds to selection pressure exerted by its host, influencing the gain, loss, or functional diversification of putative effector genes. Whole genome resequencing of 197 P. nodorum isolates collected from spring, durum, and winter wheat production regions of the United States enabled the examination of effector diversity and genomic regions under selection specific to geographically discrete populations. A total of 1,026,859 quality SNPs/InDels were identified within the natural population. Implementation of GWAS identified novel loci, as well as SnToxA and SnTox3 as major factors in disease. Genes displaying presence/absence variation and predicted effector genes, as well as genes localized on an accessory chromosome, had significantly higher pN/pS ratios, indicating a greater level of diversifying selection. Population structure analyses indicated two major P. nodorum populations corresponding to the Upper Midwest (Population 1) and Southern/Eastern United States (Population 2). Prevalence of SnToxA varied greatly between the two populations which correlated with presence of the host sensitivity gene Tsn1. Additionally, 12 and 5 candidate effector genes were observed to be diversifying among isolates from Population 1 and Population 2, respectively, but under purifying or neutral selection in the opposite population. Selective sweep analysis revealed 10 and 19 regions of positive selection from Population 1 and Population 2, respectively, with 92 genes underlying population-specific selective sweeps. Also, genes exhibiting presence/absence variation were significantly closer to transposable elements. Taken together, these results indicate that P. nodorum is rapidly adapting to distinct selection pressures unique to spring and winter wheat production regions by various routes of genomic diversification, potentially facilitated through transposable element activity.

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