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, Helen J. Bates, Fiona Wilson, Alison C. Jackson, Sascha Ott, Richard J. Harrison*, John P. Clarkson

*Corresponding author for this work

Research output: Contribution to journalArticleAcademicpeer-review

63 Citations (Scopus)

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.

Original languageEnglish
Article number13530
JournalScientific Reports
Volume8
DOIs
Publication statusPublished - 10 Sept 2018
Externally publishedYes

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