Comparative genomics reveals mobile pathogenicity chromosomes in Fusarium

Abstract

Fusarium species are among the most important phytopathogenic and toxigenic fungi. To understand the molecular underpinnings of pathogenicity in the genus Fusarium, we compared the genomes of three phenotypically diverse species: Fusarium graminearum, Fusarium verticillioides and Fusarium oxysporum f. sp. lycopersici. Our analysis revealed lineage-specific (LS) genomic regions in F. oxysporum that include four entire chromosomes and account for more than one-quarter of the genome. LS regions are rich in transposons and genes with distinct evolutionary profiles but related to pathogenicity, indicative of horizontal acquisition. Experimentally, we demonstrate the transfer of two LS chromosomes between strains of F. oxysporum, converting a non-pathogenic strain into a pathogen. Transfer of LS chromosomes between otherwise genetically isolated strains explains the polyphyletic origin of host specificity and the emergence of new pathogenic lineages in F. oxysporum. These findings put the evolution of fungal pathogenicity into a new perspective.

Figure 1. Phylogenetic relationship of four Fusarium species in relation to other ascomycete fungi and phenotypic variation among the four Fusarium species

a, Maximum-likelihood tree using concatenated protein sequences of 100 genes randomly selected from 4,694 Fusarium orthologous genes that have clear 1:1:1:1 correlation among the Fusarium genomes and have unique matches in Magnaporthe grisea, Neurospora crassa and Aspergillus nidulans. The tree was constructed with PHYML (WAG model of evolution36). Branches are labelled with the percentage of 10,000 bootstrap replicates. b–d, Phenotypic variation within the genus Fusarium: b, disease symptoms of (top to bottom) kernel rot of maize (Fv), wilt of tomato (Fol), head blight of wheat (Fg) and root rot of pea (Fs); c, the perithecial states of Fv (Gibberella moniliformis), Fol (no sexual state), Fg (G. zeae) and Fs (Nectria haematococca); and d, micro- and macroconidia of Fv, Fol, Fg and Fs. Scale bars, 10 µm. Fg produces only macroconidia.

Figure 2. Whole genome comparison between Fv and Fol

a, Argo dotplot of pair-wise MEGABLAST alignment (1 × 10⁻¹⁰) between Fv and Fol showing chromosome correspondences between the two genomes in the black dashed boxes. The vertical blue lines illustrate the chromosomal translocations, and the red dashed horizontal boxes highlight the Fol LS chromosomes. b, Global view of syntenic alignments between Fol and Fv and the distribution of transposable elements. Fol linkage groups are shown as the reference, and the length of the light grey background for each linkage group is defined by the Fol optical map. For each chromosome, row i represents the genomic scaffolds positioned on the optical linkage groups separated by scaffold breaks. Scaffold numbers for Fol are given above the blocks; row ii displays the syntenic mapping of Fv chromosomes, with one major translocation between chr 4/chr 12 in Fol and chr 4/chr 8 in Fv; row iii represents the density of transposable elements calculated with a 10 kb window. LS chromosomes include four entire chromosomes (chr 3, chr 6, chr 14 and chr 15) and parts of chromosome 1 and 2 (scaffold 27, scaffold 31), which lack similarity to syntenic chromosomes in Fv but are enriched for TEs. c, Two of the four Fol LS chromosomes showing the inter- (green) and intra- (yellow) chromosomal segmental duplications. The three traces below are density distribution of TEs (blue lines), secreted protein genes (green lines) and lipid metabolism related genes (red line). Chr, chromosome; Un, unmapped.

Figure 3. Evolutionary origin of genes on the Fol LS chromosomes

The scatter plots of BLAST score ratio (BSR) based on three-way comparisons of proteins encoded in core regions (a) and the Fol LS chromosomes (b). The numbers indicate the percentage of genes that lack homologous sequences in Fv and Fg (lower left corner), present in Fv but not Fg (x-axis) and present in Fg but not in Fv (y-axis). c, Discordant phylogenetic relationship of proteins encoded in the LS regions. The maximum-likelihood tree was constructed using the concatenated protein sequences of 100 genes randomly selected from 362 genes that share homologues in seven selected ascomycetes genomes including the four Fusarium genomes, M. grisea, N. crassa and A. nidulans. The trees were constructed with PHYML (WAG model of evolution36). The percentages for the branches represent the value based on a 10,000 bootstrapping data set.

Figure 4. Transfer of a pathogenicity chromosome

a, Tomato plants infected with Fol007, Fo-47 or double drug resistant Fo-47⁺ strains (1A through 3C) derived from this parental combination, two weeks after inoculation as described for b. b, Eight of nine Fo-47⁺ strains derived from pairing Fol007 and Fo-47 show pathogenicity towards tomato. Average disease severity in tomato seedlings was measured 3 weeks after inoculation in arbitrary units (a.u.). The overall phenotype and the extent of browning of vessels was scored on a scale of 0–4: 0, no symptoms; 1, slightly swollen and/or bent hypocotyl; 2, one or two brown vascular bundles in hypocotyl; 3, at least two brown vascular bundles and growth distortion (strong bending of the stem and asymmetric development); 4, all vascular bundles are brown, plant either dead or stunted and wilted. c, The presence of SIX genes and ORX1 in Fom, Fo-47 and Fol isolates and in double drug-resistant strains derived from co-incubation of Fol/Fom and Fol/Fo-47, assessed by PCR on genomic DNA. Co-incubations were performed with the isolates shown in bold. Three independent transformants of Fom and Fo-47 with a randomly inserted hygromycin resistance gene (H1, H2, H3) were investigated. d, Fo- 47⁺ strains derived from a Fol007/Fo-47 co-incubation have the same karyotype as Fo-47, plus one or two chromosomes from Fol007. Protoplasts from Fol4287, Fol007 (with BLE on chromosome 14), three independent HYG transformants of Fo-47 (lane Fo-47 H1, H2 and H3) and nine Fo-47⁺ strains (lane 1A to 3C, the number 1, 2 or 3 referring to theHYG resistant transformant from which they were derived) were loaded on a CHEF (contour-clamped homogeneous electric field) gel. Chromosomes of S. pombe were used as a molecular size marker. Arrows 1 and 2 point to additional chromosomes in the Fo-47⁺ strains relative to Fo-47. e, Southern blot of the CHEF gel shown in d, hybridized with a SIX6 probe, showing that chromosome 14 (arrow 1 in d) is present in all strains except Fo-47 (H1, H2 and H3).