Brenes Guallar Megan A, Fokkens Like, Rep Martijn, Berke Lidija, van Dam Peter
Bioinformatics and Software Development Team, Genetwister Technologies B.V., Wageningen, Netherlands.
Laboratory of Phytopathology, Wageningen University, Wageningen, Netherlands.
Front Plant Sci. 2022 Oct 19;13:1012688. doi: 10.3389/fpls.2022.1012688. eCollection 2022.
The fungus is infamous for its devastating effects on economically important crops worldwide. isolates are grouped into based on their ability to cause disease on different hosts. Assigning strains to using non-experimental procedures has proven to be challenging due to their genetic heterogeneity and polyphyletic nature. However, genetically diverse isolates of the same 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 Effector Clustering (FoEC) pipeline which is able to classify strains by 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 genomes and further analysis of putative effector families as multiple sequence alignments. We confirm classification of isolates into and are able to further identify their subtypes. The pipeline is available on github: https://github.com/pvdam3/FoEC2.
这种真菌因其对全球具有经济重要性的作物造成的毁灭性影响而声名狼藉。分离株根据其在不同宿主上引起疾病的能力进行分组。由于其遗传异质性和多系性质，使用非实验程序将菌株分配到不同组已被证明具有挑战性。然而，同一真菌的基因多样化分离株编码相似的效应子库，效应子是由真菌分泌的蛋白质，有助于与宿主建立亲和性。基于这一观察结果，我们之前设计了真菌效应子聚类（FoEC）流程，该流程能够仅使用基因组组装作为输入，通过对预测的假定效应子序列存在情况的层次聚类，按组对菌株进行分类。在此，我们展示更新后的FoEC2流程，它更用户友好、可定制，并且由于采用了多线程技术，具有更高的可扩展性。它被设计为一个Snakemake流程，并集成了一个新的交互式可视化应用程序。我们通过对537个公开可用的真菌基因组进行聚类以及将假定效应子家族作为多序列比对进行进一步分析，展示了FoEC2。我们确认了分离株的分组，并能够进一步识别它们的亚型。该流程可在github上获取：https://github.com/pvdam3/FoEC2。
