Comparative “Omics” of theFusarium fujikuroiSpecies Complex Highlights Differences in Genetic Potential and Metabolite Synthesis

Abstract

Species of the Fusarium fujikuroi species complex (FFC) cause a wide spectrum of often devastating diseases on diverse agricultural crops, including coffee, fig, mango, maize, rice, and sugarcane. Although species within the FFC are difficult to distinguish by morphology, and their genes often share 90% sequence similarity, they can differ in host plant specificity and life style. FFC species can also produce structurally diverse secondary metabolites (SMs), including the mycotoxins fumonisins, fusarins, fusaric acid, and beauvericin, and the phytohormones gibberellins, auxins, and cytokinins. The spectrum of SMs produced can differ among closely related species, suggesting that SMs might be determinants of host specificity. To date, genomes of only a limited number of FFC species have been sequenced. Here, we provide draft genome sequences of three more members of the FFC: a single isolate of F. mangiferae, the cause of mango malformation, and two isolates of F. proliferatum, one a pathogen of maize and the other an orchid endophyte. We compared these genomes to publicly available genome sequences of three other FFC species. The comparisons revealed species-specific and isolate-specific differences in the composition and expression (in vitro and in planta) of genes involved in SM production including those for phytohormome biosynthesis. Such differences have the potential to impact host specificity and, as in the case of F. proliferatum, the pathogenic versus endophytic life style.

Gapless genome assembly of Colletotrichum higginsianum reveals chromosome structure and association of transposable elements with secondary metabolite gene clusters

“…LTR elements are the most abundant TEs in C. higginsianum , as reported in other fungi, e.g. Cochliobolus heterostrophus , F. fujikuroi , F. oxysporum , L. maculans and V. dahliae [94–97] and several Colletotrichum species [13, 91]. Most of the DNA transposons in C. higginsianum belong to the TIR order, superfamily Tc1-Mariner.…”

The cereal pathogen Fusarium pseudograminearum produces a new class of active cytokinins during infection

“…purpurea and F . fujikuroi clusters (Hinsch et al ., ; Niehaus et al ., ), cytochrome P450 monooxygenase‐encoding genes adjacent to IPT‐LOGs were observed for all analysed Fusarium strains. However, phylogenetic analysis of cytochrome P450 monooxygenases suggested that, like IPT‐LOG, there were three sequence types (Fig.…”

“…purpurea (CPUR_04177) and two in F . fujikuroi (FFUJ_03536 and FFUJ_14354) were shown to contribute to a large proportion of the tZ pool produced by these species (Hinsch et al ., ; Niehaus et al ., ). This prompted an analysis of a broader suite of fungal genomes for sequence homologues of these genes.…”

“…fujikuroi , suggesting that the cluster, with the exception of FCK4 , may be inactive in culture, consistent with the analysis of transcriptional data for five different strains from this lineage by Niehaus et al . ().…”

“…A cytochrome P450 monooxygenase, which catalyses the iP hydroxylation to tZ, is located next to the IPT-LOG gene, forming a small cytokinin production gene cluster in this species. Two active copies of this gene cluster responsible for tZ production are also present in members of the Fusarium fujikuroi species complex (Niehaus et al, 2016).…”