Submitted to: Meeting Abstract
Publication Type: Abstract Only
Publication Acceptance Date: 7/17/2016
Publication Date: 7/17/2016
Citation: Kelly, A.C., Ward, T.J. 2016. Population genomics of Fusarium graminearum head blight pathogens in North America [abstract].
Technical Abstract: In this study we utilized comparative genomics to identify candidate adaptive alleles in the fungus Fusarium graminearum, the primary pathogen of Fusarium head blight (FHB) in cereal crops. Recent epidemics of FHB have been economically devastating to agriculture, as F. graminearum reduces cereal yield and contaminates grain with harmful mycotoxins. We performed Illumina whole-genome sequencing (50X coverage) on 60 F. graminearum strains from the U.S. and Canada, and then utilized a combination of reference-based mapping and de novo sequence assembly to assess genomic diversity and differences in gene content. Bayesian clustering and phylogenetic analyses based on 505,748 SNPs revealed three major F. graminearum populations. Isolates with the recently discovered NX-2 toxin type were genetically distinct from the resident and emergent populations that are typically associated with FHB in North America. However, 8 out of 20 NX-2 isolates shared a substantial proportion of their ancestry (63% on average) with resident isolates that have the 15ADON toxin type. High-resolution genome scans of diversity revealed multiple loci that exhibited genetic signatures consistent with adaptive divergence, in that these regions were highly differentiated among populations, had an excess of rare variants and showed reduced intrapopulation diversity. Candidate selected regions included the trichothecene toxin gene cluster encoding the core metabolic enzymes responsible for structural differences among toxin types. A second locus encoded a protein kinase (PKS3) involved in fruiting body pigmentation and a type of RNA helicase that has proven critical for cold adaptation in other fungal species. A third locus encoded four uncharacterized proteins with homology to primary metabolic enzymes. De novo assembly of unmapped reads identified 22,788 contigs (average length 618 bp) that were missing or highly diverged from the F. graminearum reference genome. Though most unmapped contigs (87%) were found in a single isolate, we detected 162 genes that were widely distributed and differentially maintained across populations. These population-enriched genes showed homology to proteins in other phytopathogenic fungi with predicted functions in secondary metabolism, fungal self/non-self recognition and fungal cell-wall degradation. Our findings suggest that cold tolerance and trichothecene toxin diversity may be driving local adaptation in F. graminearum populations. Furthermore, differences in gene content suggest that competitive interactions with other fungi and secondary metabolite diversification have shaped the population genome of F. graminearum, and may be contributing to differences in how these pathogens exploit the agricultural landscapes of North America.