Hane James K, Paxman Jonathan, Jones Darcy A B, Oliver Richard P, de Wit Pierre
Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Perth, WA, Australia.
Curtin Institute for Computation, Faculty of Science and Engineering, Curtin University, Perth, WA, Australia.
Front Microbiol. 2020 Jan 21;10:3088. doi: 10.3389/fmicb.2019.03088. eCollection 2019.
The traditional classification of fungal and oomycete phytopathogens into three classes - biotrophs, hemibiotrophs, or necrotrophs - is unsustainable. This study highlights multiple phytopathogen species for which these labels have been inappropriately applied. We propose a novel and reproducible classification based solely on genome-derived analysis of carbohydrate-active enzyme (CAZyme) gene content called CAZyme-Assisted Training And Sorting of -trophy (CATAStrophy). CATAStrophy defines four major divisions for species associated with living plants. These are monomertrophs (Mo) (corresponding to biotrophs), polymertrophs (P) (corresponding to necrotrophs), mesotrophs (Me) (corresponding to hemibiotrophs), and vasculartrophs (including species commonly described as wilts, rots, or anthracnoses). The Mo class encompasses symbiont, haustorial, and non-haustorial species. Me are divided into the subclasses intracellular and extracellular Me, and the P into broad and narrow host sub-classes. This gives a total of seven discrete plant-pathogenic classes. The classification provides insight into the properties of these species and offers a facile route to develop control measures for newly recognized diseases. Software for CATAStrophy is available online at https://github.com/ccdmb/catastrophy. We present the CATAStrophy method for the prediction of trophic phenotypes based on CAZyme gene content, as a complementary method to the traditional tripartite "biotroph-hemibiotroph-necrotroph" classifications that may encourage renewed investigation and revision within the fungal biology community.
将真菌和卵菌植物病原体传统分类为生物营养型、半活体营养型或坏死营养型这三类是不可持续的。本研究强调了多种植物病原体物种，而这些标签被不恰当地应用于它们。我们提出了一种全新且可重复的分类方法，该方法仅基于对碳水化合物活性酶（CAZyme）基因含量的基因组分析，称为CAZyme辅助的营养型训练与分类（CATAStrophy）。CATAStrophy为与活体植物相关的物种定义了四个主要类别。这些类别分别是单体营养型（Mo）（对应于生物营养型）、多聚体营养型（P）（对应于坏死营养型）、中营养型（Me）（对应于半活体营养型）和维管营养型（包括通常被描述为萎蔫、腐烂或炭疽病的物种）。Mo类别包括共生型、吸器型和非吸器型物种。Me分为细胞内和细胞外Me亚类，P分为广泛宿主和狭窄宿主亚类。这样总共就有七个离散的植物致病类别。该分类为这些物种的特性提供了见解，并为开发针对新发现疾病的控制措施提供了一条简便途径。用于CATAStrophy的软件可在https://github.com/ccdmb/catastrophy在线获取。我们提出基于CAZyme基因含量预测营养表型的CATAStrophy方法，作为传统的“生物营养型 - 半活体营养型 - 坏死营养型”三方分类的补充方法，这可能会促使真菌生物学界重新开展研究并进行修订。
