Related mobile pathogenicity chromosomes in Fusarium oxysporum determine host range on cucurbits

Dora

Sánchez-Rodríguez

et al. 2020

Preprint

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Plant pathogens cause widespread yield losses in agriculture. Understanding the drivers of plantpathogen interactions requires decoding the molecular dialog leading to either resistance or disease.However, progress in deciphering pathogenicity genes has been severely hampered by suitable model systems and incomplete fungal genome assemblies. Here, we report a significant improvement of the assembly and annotation of the genome of the Fusarium oxysporum (Fo) strain Fo5176. Fo comprises a large number of serious plant pathogens on dozens of plant species with largely unresolved pathogenicity factors. The strain Fo5176 infects Arabidopsis thaliana and, hence, constitutes a highly promising model system. We use high-coverage Pacific Biosciences Sequel long-read sequencing to assemble the genome into 19 chromosome-scale contigs with a N50 of 5 Mb and a 99.1% complete BUSCO score. Phylogenomic analyses based on single-copy orthologs clearly place the Fo5176 strain in the Fo f sp. conglutinans clade as expected. We generated RNAseq data from culture medium and plant infections to train gene predictions and identified 19'069 genes including ten effector genes known from other Fo clades. We show that Fo5176 is able to infect cabbage and Brussel sprouts of the Brassica oleracea expanding the usefulness of the Fo5176 model pathosystem. Finally, we performed large-scale comparative genomics analyses comparing the Fo5176 to 103 additional Fo genomes to define core and accessory genomic regions. In conjunction with the molecular tool sets available for A. thaliana, the Fo5176 genome and annotation provides a crucial step towards the establishment of a highly promising pathosystem.

Section: Landscape Of the Accessory Genome Across Fomentioning

confidence: 99%

A chromosome-scale genome assembly for theFusarium oxysporumstrain Fo5176 to establish a modelArabidopsis-fungal pathosystem

Dora

Sánchez-Rodríguez

et al. 2020

Preprint

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“…Fo strains infecting tomato or melon express effector genes that are associated with pathogenicity toward a specific host and these effector genes are found on distinct chromosomes (Li et al 2020;van Dam et al 2017;Armitage et al 2018;Ma et al 2010). Horizontal chromosome transfer can transform a non-pathogen recipient into a pathogenic strain on the host of the donor strain.…”

Section: ; Supplementarymentioning

confidence: 99%

“…Horizontal chromosome transfer can transform a non-pathogen recipient into a pathogenic strain on the host of the donor strain. Horizontal transfer is an important mechanism driving the evolution of pathogenicity in Fo (Ma et al 2010;van Dam et al 2017;Li et al 2020). Mobile chromosomes can readily be identified using comparative genomics by testing for matches in the phylogeny of individual chromosomes and hosts.…”

Section: ; Supplementarymentioning

confidence: 99%

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A Chromosome-Scale Genome Assembly for the Fusarium oxysporum Strain Fo5176 To Establish a Model Arabidopsis-Fungal Pathosystem

G3 Genes|Genomes|Genetics

Guo

Dora

et al. 2020

Self Cite

Plant pathogens cause widespread yield losses in agriculture. Understanding the drivers of plant-pathogen interactions requires decoding the molecular dialog leading to either resistance or disease. However, progress in deciphering pathogenicity genes has been severely hampered by suitable model systems and incomplete fungal genome assemblies. Here, we report a significant improvement of the assembly and annotation of the genome of the Fusarium oxysporum (Fo) strain Fo5176. Fo comprises a large number of serious plant pathogens on dozens of plant species with largely unresolved pathogenicity factors. The strain Fo5176 infects Arabidopsis thaliana and, hence, constitutes a highly promising model system. We use high-coverage Pacific Biosciences Sequel long-read and Hi-C sequencing data to assemble the genome into 19 chromosomes and a total genome size of 67.98 Mb. The genome has a N50 of 4 Mb and a 99.1% complete BUSCO score. Phylogenomic analyses based on single-copy orthologs clearly place the Fo5176 strain in the Fo f sp. conglutinans clade as expected. We generated RNAseq data from culture medium and plant infections to train gene predictions and identified ~18,000 genes including ten effector genes known from other Fo clades. We show that Fo5176 is able to infect cabbage and Brussel sprouts of the Brassica oleracea, expanding the usefulness of the Fo5176 model pathosystem. Finally, we performed large-scale comparative genomics analyses comparing the Fo5176 to 103 additional Fo genomes to define core and accessory genomic regions. In conjunction with the molecular tool sets available for A. thaliana, the Fo5176 genome and annotation provides a crucial step towards the establishment of a highly promising pathosystem.

“…of Fo can be distinguished based on the set of (candidate) effector genes they contain, it seems likely that effector genes contribute to host specificity (Inoue et al, 2017). Until now, individual genes that determine host specificity have not been identified in Fo, but entire chromosomes that determine host range have been identified in Fol (Ma et al, 2010;Vlaardingerbroek et al, 2016a), Forc (van Dam et al, 2017, and Fom (Li et al, 2020). For example, a single chromosome in Forc016, chr RC , is responsible for its ability to cause disease in cucumber, melon, and watermelon (van Dam et al, 2017).…”

Section: Introductionmentioning

confidence: 99%

A single gene in Fusarium oxysporum limits host range

Molecular Plant Pathology

Rep

2020

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