Bioinformatics and Genomics applications in plant pathology

Fungal plant pathogens are a major food security problem, with as few as five major species destroying stocks capable of feeding >600 million people. Many plant pathogens possess a battery of ‘effector’ molecules, usually proteins, which initiate plant disease or cicumvent host defences by either masking the presence of the pathogen or killing the host cell directly.
Effector identification is critical to developing crop resistance and their prediction largely relies on bioinformatics.

Fungi are capable of rapid adaptation to selection pressures, due largely to their genomes being inherently plastic, with multiple types of whole-genome or feature-targeted mutagenesis mechanisms acting upon their gene sequences. As such, the study of fungal genome evolution is important to inform our understanding of pathogenic adaptations, such as the compartmentalisation of pathogen genomes into stable ‘core’ segments and plastic ‘accessory’ regions. Furthermore, the high rate of mutation within accessory regions poses a challenge to traditional sequence-alignment based methods of identifying functionally-related protein families, as pathogenicity genes such as those encoding effectors rarely share recognisable
sequence homology.

This presentation is an overview of recent genome-based studies of fungal pathogens discerning the evolution of fungal pathogenicity and seeking to improve pathogenicity effector prediction using genomic information.

James Hane

Dr James Hane

Senior Research Fellow, Centre for Crop & Disease Management, Curtin University

James studied for a Ph. D. with Prof. Richard Oliver at the Australian Centre for Necrotrophic Fungal Pathogens, then did post-doctoral research at CSIRO with Prof. Karam Singh’s Molecular plant pathology and genomics group, before joining the Centre for Crop and Disease Management at Curtin in 2014. His research involves genome analysis of agriculturally-important fungal pathogens and host crop species, and bioinformatic investigation of their evolution and underlying biology of their interactions during infection. This has included the first genome analysis for several pathogen species of agricultural and economic importance, defining a broad genetic basis for the biological activities of these organisms and facilitating subsequent studies that apply highthroughput reverse genetics approaches to the study of these species. These new genomic resources have also been applied to comparative genomics, which has contributed novel insights in the field of fungal genomics, including first observations of a fungal-specific conservation pattern ‘mesosynteny’; the study of a fungal-specific mutagenesis process called repeat-induced point mutation (RIP) ; and investigations of lateral gene transfers between fungal species and other plant-associated species. These features of fungal genomes are the major drivers of their evolution and form the basis for ongoing research into pathogenicity adaptation and developing informed bioinformatics methods to accurately predict the fungal genes that cause plant disease.

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