DataSheet_4_Fusarium oxysporum effector clustering version 2: An updated pipeline to infer host range.pdf

The fungus Fusarium oxysporum is infamous for its devastating effects on economically important crops worldwide. F. oxysporum isolates are grouped into formae speciales based on their ability to cause disease on different hosts. Assigning F. oxysporum strains to formae speciales using non-experimental procedures has proven to be challenging due to their genetic heterogeneity and polyphyletic nature. However, genetically diverse isolates of the same forma specialis encode similar repertoires of effectors, proteins that are secreted by the fungus and contribute to the establishment of compatibility with the host. Based on this observation, we previously designed the F. oxysporum Effector Clustering (FoEC) pipeline which is able to classify F. oxysporum strains by forma specialis based on hierarchical clustering of the presence of predicted putative effector sequences, solely using genome assemblies as input. Here we present the updated FoEC2 pipeline which is more user friendly, customizable and, due to multithreading, has improved scalability. It is designed as a Snakemake pipeline and incorporates a new interactive visualization app. We showcase FoEC2 by clustering 537 publicly available F. oxysporum genomes and further analysis of putative effector families as multiple sequence alignments. We confirm classification of isolates into formae speciales and are able to further identify their subtypes. The pipeline is available on github: https://github.com/pvdam3/FoEC2.

尖孢镰刀菌（Fusarium oxysporum）因对全球范围内具有经济重要性的农作物造成毁灭性危害而臭名昭著。该真菌的分离株根据其在不同宿主上引发病害的能力被划分为专化型（formae speciales）。由于其遗传异质性与多系演化特性，通过非实验方法将尖孢镰刀菌菌株归类至相应专化型一直是一项难题。然而，同一专化型的遗传多样性分离株会编码相似的效应蛋白（effectors）组库；这类蛋白由真菌分泌，有助于建立与宿主的亲和互作。基于这一发现，我们此前开发了尖孢镰刀菌效应蛋白聚类（Fusarium oxysporum Effector Clustering, FoEC）流程，该流程仅需基因组组装结果作为输入，通过对预测的假定效应蛋白序列的存在情况进行层次聚类，即可按照专化型对尖孢镰刀菌菌株进行分类。本研究介绍了更新后的FoEC2流程，该流程更具用户友好性、可定制性，且由于采用多线程技术，其可扩展性得到了提升。该流程基于Snakemake框架开发，并集成了一款全新的交互式可视化应用程序。我们通过对537株公开可用的尖孢镰刀菌基因组进行聚类，并对假定效应蛋白家族开展多序列比对分析，对FoEC2流程进行了性能验证。本研究验证了分离株的专化型分类结果，并可进一步识别其亚型。该流程的开源代码托管于GitHub：https://github.com/pvdam3/FoEC2。