Lifestyle Transitions in Fusarioid Fungi are Frequent and Lack Clear Genomic Signatures.

Hill, Rowena; Buggs, Richard J.A.; Vu, Dang Toan; Gaya, Ester

Lifestyle Transitions in Fusarioid Fungi are Frequent and Lack Clear Genomic Signatures.

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Journal article

Creator (person)

Hill, Rowena

Buggs, Richard J.A.

Vu, Dang Toan

Gaya, Ester

Date published

April 1, 2022

Abstract

The fungal genus Fusarium (Ascomycota) includes well-known plant pathogens that are implicated in diseases worldwide, and many of which have been genome sequenced. The genus also encompasses other diverse lifestyles, including species found ubiquitously as asymptomatic-plant inhabitants (endophytes). Here, we produced structurally annotated genome assemblies for five endophytic Fusarium strains, including the first whole-genome data for Fusarium chuoi. Phylogenomic reconstruction of Fusarium and closely related genera revealed multiple and frequent lifestyle transitions, the major exception being a monophyletic clade of mutualist insect symbionts. Differential codon usage bias and increased codon optimisation separated Fusarium sensu stricto from allied genera. We performed computational prediction of candidate secreted effector proteins (CSEPs) and carbohydrate-active enzymes (CAZymes)—both likely to be involved in the host–fungal interaction—and sought evidence that their frequencies could predict lifestyle. However, phylogenetic distance described gene variance better than lifestyle did. There was no significant difference in CSEP, CAZyme, or gene repertoires between phytopathogenic and endophytic strains, although we did find some evidence that gene copy number variation may be contributing to pathogenicity. Large numbers of accessory CSEPs (i.e., present in more than one taxon but not all) and a comparatively low number of strain-specific CSEPs suggested there is a limited specialisation among plant associated Fusarium species. We also found half of the core genes to be under positive selection and identified specific CSEPs and CAZymes predicted to be positively selected on certain lineages. Our results depict fusarioid fungi as prolific generalists and highlight the difficulty in predicting pathogenic potential in the group.

Creator (organisation)

Hill, Rowena

Buggs, Richard J.A.

Vu, Dang Toan

Gaya, Ester

Contributor (person)

Hepp, Crystal

Project(s)

Priority 4: Accelerated Taxonomy

Priority 2: Trait Diversity and Function

Funder

Funder name	Awards
Evolution and Education Trust
Pragnell Fund
Natural Environment Research Council, United Kingdom	London NERC DTP (NERC Ref: NE/L002485/1)