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Aspergillus fumigatus is a deadly agent of human fungal disease where virulence heterogeneity is thought to be at least partially structured by genetic variation between strains. While population genomic analyses based on reference genome alignments offer valuable insights into how gene variants are distributed across populations, these approaches fail to capture intraspecific variation in genes absent from the reference genome. Pan-genomic analyses based on de novo assemblies offer a promising alternative to reference-based genomics with the potential to address the full genetic repertoire of a species. Here, we evaluate 260 genome sequences of A . fumigatus including 62 newly sequenced strains, using a combination of population genomics, phylogenomics, and pan-genomics. Our results offer a high-resolution assessment of population structure and recombination frequency, phylogenetically structured gene presence–absence variation, evidence for metabolic specificity, and the distribution of putative antifungal resistance genes. Although A . fumigatus disperses primarily via asexual conidia, we identified extraordinarily high levels of recombination with the lowest linkage disequilibrium decay value reported for any fungal species to date. We provide evidence for 3 primary populations of A . fumigatus , with recombination occurring only rarely between populations and often within them. These 3 populations are structured by both gene variation and distinct patterns of gene presence–absence with unique suites of accessory genes present exclusively in each clade. Accessory genes displayed functional enrichment for nitrogen and carbohydrate metabolism suggesting that populations may be stratified by environmental niche specialization. Similarly, the distribution of antifungal resistance genes and resistance alleles were often structured by phylogeny. Altogether, the pan-genome of A . fumigatus represents one of the largest fungal pan-genomes reported to date including many genes unrepresented in the Af293 reference genome. These results highlight the inadequacy of relying on a single-reference genome-based approach for evaluating intraspecific variation and the power of combined genomic approaches to elucidate population structure, genetic diversity, and putative ecological drivers of clinically relevant fungi. 

Abstract Fungal conservation is gaining momentum globally, but many challenges remain. To advance further, more data are needed on fungal diversity across space and time. Fundamental information regarding population sizes, trends, and geographic ranges is also critical to accurately assess the extinction risk of individual species. However, obtaining these data is particularly difficult for fungi due to their immense diversity, complex and problematic taxonomy, and cryptic nature. This paper explores how citizen science (CS) projects can be leveraged to advance fungal conservation efforts. We present several examples of past and ongoing CS‐based projects to record and monitor fungal diversity. These include projects that are part of broad collecting schemes, those that provide participants with targeted sampling methods, and those whereby participants collect environmental samples from which fungi can be obtained. We also examine challenges and solutions for how such projects can capture fungal diversity, estimate species absences, broaden participation, improve data curation, and translate resulting data into actionable conservation measures. Finally, we close the paper with a call for professional mycologists to engage with amateurs and local communities, presenting a framework to determine whether a given project would likely benefit from participation by citizen scientists. 

Summary Research on mycorrhizal symbiosis has been slowed by a lack of established study systems. To address this challenge, we have been developingSuillus, a widespread ecologically and economically relevant fungal genus primarily associated with the plant family Pinaceae, into a model system for studying ectomycorrhizal (ECM) associations. Over the last decade, we have compiled extensive genomic resources, culture libraries, a phenotype database, and protocols for manipulatingSuillusfungi with and without their tree partners. Our efforts have already resulted in a large number of publicly available genomes, transcriptomes, and respective annotations, as well as advances in our understanding of mycorrhizal partner specificity and host communication, fungal and plant nutrition, environmental adaptation, soil nutrient cycling, interspecific competition, and biological invasions. Here, we highlight the most significant recent findings enabled bySuillus, present a suite of protocols for working with the genus, and discuss howSuillusis emerging as an important model to elucidate the ecology and evolution of ECM interactions.