Cross-Disciplinary Genomics Approaches to Studying Emerging Fungal Infections

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.

Whole‐mitochondrial genomes of Nannizziopsis provide insights in evolution and detection

“…Diseases‐causing fungi pose a serious threat to wildlife populations, yet despite the impact they have had on global biodiversity, they are notably understudied (Ghosh et al, 2018 ). New fungal pathogens are emerging that are capable of infecting an increasingly diverse range of taxa and their impacts are being exacerbated by changing climate conditions and globalization (Fisher et al, 2012 ; Ghosh et al, 2020 ). Urbanization can be a key driver of disease emergence, facilitating transmission due to newly overlapping geographic expansions (Hassell et al, 2017 ), increasing the risk of disease spillover from wildlife into humans and other animals (Heesterbeek et al, 2015 ).…”

“…Such tools also enable long‐term tracking of pathogens that facilitate the study of often complex host–pathogen interactions, such as how disease tolerance may effect prevalence and transmission (Seal et al, 2021 ; Tedersoo et al, 2019 ). Genomic data are valuable resources for the development of diagnostic tools enabling swift identification of target regions for designing highly specific markers, and these data can also serve as a foundation for studies on the molecular basis for pathogen evolution (DeCandia et al, 2018 ; Ghosh et al, 2020 , 2021 ). Comparative genomic studies using whole‐mitochondrial genomes, as opposed to metabarcoding, can help to resolve evolutionary relationships by building more robust phylogenies in newly described species and thus may enhance the effectiveness of species‐specific detection methods (Tedersoo et al, 2019 ).…”

“…Such tools also enable long-term tracking of pathogens that facilitate the study of often complex host-pathogen interactions, such as how disease tolerance may effect prevalence and transmission (Seal et al, 2021;Tedersoo et al, 2019). Genomic data are valuable resources for the development of diagnostic tools enabling swift identification of target regions for designing highly specific markers, and these data can also serve as a foundation for studies on the molecular basis for pathogen evolution (DeCandia et al, 2018;Ghosh et al, 2020Ghosh et al, , 2021.…”

“…Diseases-causing fungi pose a serious threat to wildlife populations, yet despite the impact they have had on global biodiversity, they are notably understudied (Ghosh et al, 2018). New fungal pathogens are emerging that are capable of infecting an increasingly diverse range of taxa and their impacts are being exacerbated by changing climate conditions and globalization (Fisher et al, 2012;Ghosh et al, 2020).…”

Genetic mechanisms and biological processes underlying host response to ophidiomycosis (Snake Fungal Disease) inferred from tissue-specific transcriptome analyses

“…We describe the genetic and physiological changes in multiple tissues due to O. ophidiicola exposure and also the effect of different temperatures by comparing the changes in transcriptome profiles of different organs under different conditions. Finally, we identified a list of candidate genes that are putatively involved in host response which could be used in diagnostic screening of more vulnerable populations and species of snakes, as done in Bd and other wildlife diseases (49).…”