Abstract
The study of fungal physiology is set to change dramatically in the next few years as highly scalable technologies are deployed allowing accurate measurement and identification of metabolites, proteins and transcripts within cells. The advent of next-generation DNA-sequencing technologies will also provide genome sequence information from large numbers of industrially relevant and pathogenic fungal species, and allow comparative genome analysis between strains and populations of fungi. When coupled with advances in gene functional analysis, protein-protein interaction studies, live cell imaging and mathematical modelling, this promises a step-change in our understanding of how fungal cells operate as integrated dynamic living systems.
Highlights
While some fungi are beneficial to humankind, for instance in the production of antibiotics, food and beverages, many interactions between human populations and fungi have serious and negative socio-economic outcomes
Even more rapid DNA sequencing technologies are promised by a number of companies, promising ever faster and cheaper means of acquiring fungal genomic information. We envisage that these new sequencing approaches will be key to identifying the core inventory of genes in both freeliving and symbiotic fungal species, including pathogenicity-associated gene functions in human and plant fungal pathogens and the diverse set of genes encoding enzymes involved in secondary metabolic pathways, all of which are likely to be highly diverse in fungi
Comparative genome analysis and functional genomics provide information on only a subset of the interactions that are occurring during growth and development in a living cell
Summary
While some fungi are beneficial to humankind, for instance in the production of antibiotics, food and beverages, many interactions between human populations and fungi have serious and negative socio-economic outcomes. Even more rapid DNA sequencing technologies are promised by a number of companies (for example, Pacific Biosciences and their single-molecule real-time detection technology), promising ever faster and cheaper means of acquiring fungal genomic information We envisage that these new sequencing approaches will be key to identifying the core inventory of genes in both freeliving and symbiotic fungal species, including pathogenicity-associated gene functions in human and plant fungal pathogens and the diverse set of genes encoding enzymes involved in secondary metabolic pathways (as demonstrated by Yadav et al, 2009), all of which are likely to be highly diverse in fungi. Fungal physiology – a future perspective identified These genes are ideal candidates for functional analysis, as they represent putative effectors that may be deployed to suppress host defences or bring about pathogen entry, but are targeted by the host and may trigger cultivar-specific resistance in plants, or immune responses in human pathogens. Massively parallel sequencing will be applied to the discovery of small RNAs (Ghildiyal & Zamore, 2009) and the role they play in fungal physiology, chromatin immuno-precipitation studies and the elucidation of transcription regulatory networks in fungal development (Mitchell et al, 2009), and the role of epigenetic gene regulation in fungal development, physiology and virulence via genome-wide methylation analysis as recently demonstrated for plants (Corkus et al, 2008)
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