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

Abstract

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.

Segmental duplications drive the evolution of accessory regions in a major crop pathogen

“…Effector gene repertoires define host range (van Dam et al ., 2016; Brenes Guallar et al ., 2022), and we anticipated that effector presence‐absence profiles would distinguish F. oxysporum strains infecting banana from F. oxysporum strains infecting other hosts. We predicted candidate effector genes in all 124 F. oxysporum isolates based on their proximity to MIMP elements that are known to co‐localize with some effector genes in F. oxysporum (van Dam et al ., 2016; Brenes Guallar et al ., 2022), which yielded 398 MIMP‐associated effector gene families (160 of these were predicted in the complete set of 739 candidate effectors). The predicted MIMP‐associated effector repertoires clustered F. oxysporum isolates in host range (van Dam et al ., 2016; Brenes Guallar et al ., 2022; Fig.…”

“…We predicted candidate effector genes in all 124 F. oxysporum isolates based on their proximity to MIMP elements that are known to co‐localize with some effector genes in F. oxysporum (van Dam et al ., 2016; Brenes Guallar et al ., 2022), which yielded 398 MIMP‐associated effector gene families (160 of these were predicted in the complete set of 739 candidate effectors). The predicted MIMP‐associated effector repertoires clustered F. oxysporum isolates in host range (van Dam et al ., 2016; Brenes Guallar et al ., 2022; Fig. 5).…”

“…By contrast, R1 strains are genetically diverse, which is possibly due to prolonged co‐evolution of R1 strains with a plethora of genetically diverse banana varieties in the center of origin in Southeast Asia (Perrier et al ., 2011). Extensive genetic diversity among F. oxysporum strains that infect the same host is not uncommon (Baayen et al ., 2000; van Dam et al ., 2016; Henry et al ., 2021; Fayyaz et al ., 2023), yet their ARs and effector profiles are typically remarkably similar (van Dam et al ., 2016; Fokkens et al ., 2018; Brenes Guallar et al ., 2022). We, however, observe that the ARs and effector profile of R1 strains show extensive variation, underscoring their diversity and possibly suggesting that different mechanisms contribute to disease in banana (Henry et al ., 2021; Brenes Guallar et al ., 2022).…”

“…Extensive genetic diversity among F. oxysporum strains that infect the same host is not uncommon (Baayen et al ., 2000; van Dam et al ., 2016; Henry et al ., 2021; Fayyaz et al ., 2023), yet their ARs and effector profiles are typically remarkably similar (van Dam et al ., 2016; Fokkens et al ., 2018; Brenes Guallar et al ., 2022). We, however, observe that the ARs and effector profile of R1 strains show extensive variation, underscoring their diversity and possibly suggesting that different mechanisms contribute to disease in banana (Henry et al ., 2021; Brenes Guallar et al ., 2022). F. oxysporum strains that infect strawberry have two distinct ARs, one that contributes to yellowing and the other to wilting (Henry et al ., 2021).…”

Comparative genomics and transcriptomics reveal differences in effector complement and expression between races ofFusarium oxysporumf.sp.lactucae

“…As highlighted previously, miniature impala elements (mimps) have been used previously to predict potential effectors in F. oxysporum including the majority of SIX genes in different F. oxysporum f.spp. (Armitage et al, 2018, Brenes Guallar et al, 2022, Schmidt et al, 2013. We therefore adapted a mimp-associated effector identification pipeline as utilised by van Dam et al, (2016), to find putative effectors in genomes of all the Fola isolates and other F. oxysporum f.spp.…”