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

Abstract

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.

Putative Novel Effector Genes Revealed by the Genomic Analysis of the Phytopathogenic Fungus Fusarium oxysporum f. sp. physali (Foph) That Infects Cape Gooseberry Plants

“…Recent genome analysis with a chromosome-scale assembly of the brassicas infecting f. sp. Fo5176, showed a similar pattern of phylogenetic relationship possibly associated to the expansion of their host range ( Fokkens et al, 2020 ). Here, we performed comparative genomics using the Foph_ MAP5 genome assembly in order to test whether a set of available genomes of Solanaceous-infecting formae speciales including Foph , could show a similar phylogenetic related pattern.…”

Genomic differences between the new Fusarium oxysporum f. sp. apii (Foa) race 4 on celery, the less virulent Foa races 2 and 3, and the avirulent on celery f. sp. coriandrii

“…Results are shown in the text hypothetical protein of F. oxysporum f. sp. conglutinans [22] and f. sp. cepae [23], respectively.…”

A pair of effectors encoded on a conditionally dispensable chromosome ofFusarium oxysporumsuppress host-specific immunity

“…The final assembly consisted of scaffolds (SCs) with an N50 SC length of 4,865 kb and a 99.1% complete BUSCO score (Table 1). For gene prediction, we generated transcriptome data from axenic culture and plant infections, resulting in a total of 21,781 genes, among which are eight presumptive effector genes (SIX1, SIX4, SIX8, SIX9 and FOA1-FOA4) that were previously known from Arabidopsis-infecting F. oxysporum 16 , as well as the homologous genes of FOA1 and FOA4, which were named FOA1b and FOA4b, respectively. To find unknown effectors, 1,467 putative secreted proteins were screened for proteins with an effector-like structure using the EffectorP v1 and/or v2 algorithm 17,18 .…”

“…Recently, a chromosome-level genome assembly of the Arabidopsis-infecting F. oxysporum isolate Fo5176 was reported 21 . The genomes of FocnCong:1-1 and Fo5176 are very similar, sharing from 93.2% to 94.3% of their total scaffold/contig lengths (> 95% identity, 10 kb).…”

“…Next, we investigated whether the SIX8-PSE1 pair is conserved in Arabidopsis-infecting F. oxysporum isolates. Comparative analysis of highly contiguous and available genome assemblies of F. oxysporum isolates (Supplementary Table 1) 6,7,21,[30][31][32][33][34] showed that the SIX8-PSE1 locus is completely conserved in Fo5176 and in the stock-infecting pathogen F. oxysporum f. sp. matthiolae (Fomt) PHW726, which can infect Arabidopsis 13,35 , but not in isolates that cannot infect Arabidopsis (Fig.…”