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

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 ali...

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Bibliographic Details
Published in:Scientific reports 2018-09, Vol.8 (1), p.13530-15, Article 13530
Main Authors: Armitage, Andrew D., Taylor, Andrew, Sobczyk, Maria K., Baxter, Laura, Greenfield, Bethany P. J., Bates, Helen J., Wilson, Fiona, Jackson, Alison C., Ott, Sascha, Harrison, Richard J., Clarkson, John P.
Format: Article
Language:English
Subjects:
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631/181/757
631/326/421
Basal rot
Chromosomes
Fusarium oxysporum
Gene regulation
Genomes
Humanities and Social Sciences
multidisciplinary
Pathogens
Phylogeny
Ribonucleic acid
RNA
Science
Science (multidisciplinary)
Synteny
Transcription factors
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Summary: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 .
ISSN:2045-2322
2045-2322
DOI:10.1038/s41598-018-30335-7