From Fields to Genomes: Towards a Comprehensive Understanding of the Lifestyle and Evolution of Claviceps purpurea the Ergot Fungus

Claviceps purpurea (ergot), an ascomycete and member of the family Clavicipitacea, is considered a pathogen of all grass species (family Poaecea) including economically important cereal crops which infects ovaries resulting in the development of a fungal sclerotium rather than a plant seed. Ergot infections poses significant impacts to agriculture and livestock due to various toxic alkaloids present in the sclerotia. Severe ergot poisoning in humans and livestock, ergotism, can cause corrosion/loss of extremities from gangrene, internal bleeding, diarrhea, and reduced pregnancy and abortion. Due to these serious health concerns, strict restrictions are placed on the amount of ergot contaminated grain that can be accepted for food and livestock feed. However, these toxic alkaloids are also heavily researched in the field of pharmacology and have been shown to provide some beneficial aspects in human medicine. Despite the abundance of pharmacological and agricultural research on C. purpurea researchers have been unsuccessful in identifying crop or wild grass varieties that have resistance to ergot infection, leading to critical challenges in the control of ergot disease outbreaks. Recent studies have also suggested that C. purpurea is more of a conditional defensive mutualist as opposed to a plant pathogen. Taken together, these factors demonstrate that there are still gaps of knowledge surrounding the epidemiology, lifestyle, evolution, and adaptability of this species. We implemented a comprehensive analysis into the life history of C. purpurea through a combination of field surveys, greenhouse inoculations, and deep genomic data mining to help elucidate these gaps. Field surveys were conducted to investigate the role wild grass populations surrounding cereal crop fields play in epidemiology of ergot outbreaks. Results revealed that unmanaged grasses along ditch banks, even in drought years, represent significant inoculum reservoirs of ergot, particularly when Bromus spp. are present, and should be a focal point in future research for better disease control. Greenhouse inoculations were conducted to elucidate the effects of C. purpurea infections on hosts through inoculations of a single isolate on two commercial cereal crops in a controlled setting. Our results show that the effect of C. purpurea infections can range from negative to positive, depending on infection rate, plant species, and plant tissue, but overall showed a general trend of neutral effects. However, we did observe a potential for increased root growth as infection rates increased, which could signify an interesting plant-microbe interaction that imparts a benefit, of infection, on highly rhizomatous grass hosts such as Bromus spp.. Lastly, through a collaborative effort we sequenced, assembled, and annotated 50 Claviceps genomes, representing 21 species, for a comprehensive comparison of genome architecture, plasticity, and evolution within the genera. We also conducted a detailed analysis of C. purpurea through construction of a pangenome and investigations of the recombination and positive selection landscape across the genome. Our genus-wide comparison revealed that despite having nearly identical life-strategies, these closely related species have substantially altered genomic architectures and plasticity that are likely driving genome adaptation. One key difference we observed was a shift from characteristic one-speed genomes in narrow host-range Claviceps species of sections Citrinae and Paspalorum to two-speed genomes in broader host-range lineages of sections Pusillae and Claviceps. Claviceps purpurea was observed to have a large accessory genome that is likely influenced by a large effective population size, high recombination rates, and transposable element (TE) mediated gene duplication. Due to a lack of repeat-point induced (RIP) mutation, prolific TE expansion is likely controlled by high recombination rates, which subsequently may be influencing the overall trend of purifying selection observed within the species. However, secondary metabolites genes were found to have the highest rates of positive selection on codons within genes, indicating that these genes are a primary factor affecting the diversification of the species into new ecological niches and to potentially help maintain its global distribution and broad host range