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How many types of fungal & oomycete phytopathogens are there? Catastrophy for the bio/hemi/necrotroph divisions

Richard Oliver: Curtin University

<div>The classification model that dominates plant pathology is that diseases and pathogens can be divided into three ‘trophic’ classes, biotroph, hemibiotroph and necrotroph. This pathogen classification leaves much to be desired. Many pathogens are placed by different authors in two or even all three of these classes. Apart from the undisputed fact that all obligate pathogens are all biotrophic, no phenotypic feature can be described as diagnostic. Other pathogens, such as the wilts and those causing root diseases do not obviously comply with the biotroph/hemi/necrotroph trichotomy. There are now 137 fungal and oomycete pathogen genome sequences. With this information resource, we set out to determine whether an objective analysis of these genomic resources could provide a more robust classification system that had predictive power. We propose a novel bioinformatic technique for the assessment of fungal trophic phenotypes across multiple species via analysis solely of their gene content. We used the functional annotations of carbohydrate active enzymes (CAZyme). Our analysis led us to conclude that the existing tripartite trophic classification system for filamentous plant pathogens is unsustainable. Instead our analysis identified eight pathogen trophic descriptors and a saprobe trophic class. This study highlights some longstanding anomalies and permits the objective prediction of properties of a species based solely on its CAZyme gene content. We have used the data included in this study to develop and train a predictive tool for CAZyme-Assisted Training And Sorting of TROPHY - CATASTROPHY.</div>