AUTHOR=Brenes Guallar Megan A. , Fokkens Like , Rep Martijn , Berke Lidija , van Dam Peter 

TITLE=Fusarium oxysporum effector clustering version 2: An updated pipeline to infer host range

JOURNAL=Frontiers in Plant Science

VOLUME=13

YEAR=2022

URL=https://www.frontiersin.org/journals/plant-science/articles/10.3389/fpls.2022.1012688

DOI=10.3389/fpls.2022.1012688

ISSN=1664-462X

ABSTRACT=<p>The fungus <italic>Fusarium oxysporum</italic> is infamous for its devastating effects on economically important crops worldwide. <italic>F. oxysporum</italic> isolates are grouped into <italic>formae speciales</italic> based on their ability to cause disease on different hosts. Assigning <italic>F. oxysporum</italic> strains to <italic>formae speciales</italic> using non-experimental procedures has proven to be challenging due to their genetic heterogeneity and polyphyletic nature. However, genetically diverse isolates of the same <italic>forma specialis</italic> 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 <italic>F. oxysporum</italic> Effector Clustering (FoEC) pipeline which is able to classify <italic>F. oxysporum</italic> strains by <italic>forma specialis</italic> 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 <italic>F. oxysporum</italic> genomes and further analysis of putative effector families as multiple sequence alignments. We confirm classification of isolates into <italic>formae speciales</italic> and are able to further identify their subtypes. The pipeline is available on github: <uri xlink:href="https://github.com/pvdam3/FoEC2" xmlns:xlink="http://www.w3.org/1999/xlink">https://github.com/pvdam3/FoEC2</uri>.</p>