Abstract
Emerging fungal pathogens pose a serious, global and growing threat to food supply systems, wild ecosystems, and human health. However, historic chronic underinvestment in their research has resulted in a limited understanding of their epidemiology relative to bacterial and viral pathogens. Therefore, the untargeted nature of genomics and, more widely, -omics approaches is particularly attractive in addressing the threats posed by and illuminating the biology of these pathogens. Typically, research into plant, human and wildlife mycoses have been largely separated, with limited dialogue between disciplines. However, many serious mycoses facing the world today have common traits irrespective of host species, such as plastic genomes; wide host ranges; large population sizes and an ability to persist outside the host. These commonalities mean that -omics approaches that have been productively applied in one sphere and may also provide important insights in others, where these approaches may have historically been underutilised. In this review, we consider the advances made with genomics approaches in the fields of plant pathology, human medicine and wildlife health and the progress made in linking genomes to other -omics datatypes and sets; we identify the current barriers to linking -omics approaches and how these are being underutilised in each field; and we consider how and which -omics methodologies it is most crucial to build capacity for in the near future.
Highlights
Emerging fungal pathogens and outbreaks of fungal disease pose serious yet often underappreciated threats to food security, wildlife populations, and human health
For progress across all fields, in crop health and human health as well, a focused effort to apply a sophisticated -omics approach to researching wildlife pathogens could lead to great cross-disciplinary benefits and crucial insights into how the most dangerous mycoses known have evolved and interact with their hosts and environment
The plant pathology sector continues to be at the forefront of the field in terms of applying -omics approaches to understand and tackle emerging mycoses
Summary
Emerging fungal pathogens and outbreaks of fungal disease pose serious yet often underappreciated threats to food security, wildlife populations, and human health. Following its discovery in 2006 [56,73] and description in 2009 [73], multiple studies have already reported analyses of the host microbiome, comparative genomic analyses and host-specific transcriptomic responses to infection Whether this rapidity can be increased again in response to other more recently emerging fungal pathogens remains to be seen; Snake Fungal Disease (SFD), caused by Ophidiomyces ophiodiicola (Oo), was first recorded in 2006 as a syndrome of unknown aetiology causing anorexia, lesions and poor body conditions in threatened wild snakes primarily in North. Despite wildlife pathogen systems being far more amenable to an experimental approach informed by -omics than human fungal pathosystems, most studies remain correlative rather than investigating causation, unlike in plants where experimental work is pushing frontiers This lack of research investment is short-sighted, as evidenced by the catastrophic impacts inflicted on wildlife populations, in a very short space of time, by WNS and chytridiomycosis. For progress across all fields, in crop health and human health as well, a focused effort to apply a sophisticated -omics approach to researching wildlife pathogens could lead to great cross-disciplinary benefits and crucial insights into how the most dangerous mycoses known have evolved and interact with their hosts and environment
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