Comparative “omics” of the Fusarium fujikuroi species complex highlights differences in genetic potential and metabolite synthesis

Authors: MUNSTERKOTTER, MARTIN - German Research Center For Environmental Health; NIEHAUS, EVA-MARIA - University Of Munster; Proctor, Robert; Brown, Daren; SHARON, AMIR - Tel Aviv University; IDAN, YIFAT - Tel Aviv University; OREN-YOUNG, LIAT - Tel Aviv University; SIEBER, CHRISTIAN - German Research Center For Environmental Health; NOVAK, ONDREJ - Palacky University; PENCIK, ALES - Palacky University

Submitted to: Genome Biology and Evolution
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 10/21/2016
Publication Date: 11/9/2016
Citation: Niehaus, E.-M., Munsterkotter, M., Proctor, R.H., Brown, D.W., Sharon, A., Idan, Y., Oren-Young, L., Sieber, C.M., Novak, O., Pencik, A., et al. 2016. Comparative “omics” of the Fusarium fujikuroi species complex highlights differences in genetic potential and metabolite synthesis. Genome Biology and Evolution. 8(11):3574–3599.

Interpretive Summary: The Fusarium fujikuroi species complex consists of over 50 closely related fungal species that collectively cause disease on diverse agricultural crops, although individual species usually predominate on one or a few crops. Little is known about the genetic, biochemical, and physiological mechanisms that affect host specificity of members of this complex. Therefore, we conducted comprehensive genomic, transcriptomic, and metabolomic comparisons of six members that occur on diverse crops: mango, maize, orchid, pine, or rice. We identified differences in: distribution of secondary metabolite gene clusters, including mycotoxins and phytohormones; expression of some clusters; secondary metabolite production; and content of putative host specific secreted proteins. We demonstrated that the fusaria examined each have biosynthetic genes for two to three classes of phytohormones (auxins, cytokinins, and gibberellins) and produce at least low levels of the hormones. We also found that the maize plant responds to the different fusaria by activating common and species/strain-specific sets of genes, of which some can affect hormone levels. Together, our results begin to define differences between closely related Fusarium species that impact their ability to cause disease on different plant species and open up new avenues of research aimed at reducing crop diseases and improving food security and safety.

Technical 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.