Characterisation of pathogen-specific regions and novel effector candidates in Fusarium oxysporum f. sp. cepae

Andrew D Armitage,Andrew Taylor,Maria K Sobczyk,Laura Baxter,Bethany P J Greenfield,Richard J Harrison,Sascha Ott,Fiona Wilson,Alison C Jackson,John P Clarkson,Helen J Bates

doi:10.1038/s41598-018-30335-7

Andrew D Armitage, Andrew Taylor + Show 9 more

Open Access

https://doi.org/10.1038/s41598-018-30335-7

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Abstract

A reference-quality assembly of Fusarium oxysporum f. sp. cepae (Foc), the causative agent of onion basal rot has been generated along with genomes of additional pathogenic and non-pathogenic isolates of onion. Phylogenetic analysis confirmed a single origin of the Foc pathogenic lineage. Genome alignments with other F. oxysporum ff. spp. and non pathogens revealed high levels of syntenic conservation of core chromosomes but little synteny between lineage specific (LS) chromosomes. Four LS contigs in Foc totaling 3.9 Mb were designated as pathogen-specific (PS). A two-fold increase in segmental duplication events was observed between LS regions of the genome compared to within core regions or from LS regions to the core. RNA-seq expression studies identified candidate effectors expressed in planta, consisting of both known effector homologs and novel candidates. FTF1 and a subset of other transcription factors implicated in regulation of effector expression were found to be expressed in planta.

Highlights

A reference-quality assembly of Fusarium oxysporum f. sp. cepae (Foc), the causative agent of onion basal rot has been generated along with genomes of additional pathogenic and non-pathogenic isolates of onion
Three pathogenic Foc (Fus[2, 125], A23) and four non-pathogenic Fo isolates (A13, A28, PG, CB3) from onion were selected for whole genome sequencing based upon previous work[12]
Chromosomes has been revealed in the onion basal rot pathogen F. oxysporum f. sp. cepae through comparison with F. oxysporum f. sp. lycopersci

Summary

Introduction

A reference-quality assembly of Fusarium oxysporum f. sp. cepae (Foc), the causative agent of onion basal rot has been generated along with genomes of additional pathogenic and non-pathogenic isolates of onion. Cepae (Foc), the causative agent of onion basal rot has been generated along with genomes of additional pathogenic and non-pathogenic isolates of onion. Phylogenetic analysis confirmed a single origin of the Foc pathogenic lineage. Spp. and non pathogens revealed high levels of syntenic conservation of core chromosomes but little synteny between lineage specific (LS) chromosomes. In Fusarium and other fungal phytopathogens these may be specific areas of conserved ‘core’ chromosomes and individual lineage-specific ‘LS’ chromosomes, known as dispensable or supernumerary chromosomes[1]. The fungal pathogen Fusarium oxysporum (Fo) represents a diverse group of formae speciales Many Fo isolates are non-pathogenic soil saprophytes and some have even been exploited as biocontrol agents[7,8]

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