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ARS Home » Midwest Area » Peoria, Illinois » National Center for Agricultural Utilization Research » Mycotoxin Prevention and Applied Microbiology Research » Research » Publications at this Location » Publication #350439

Research Project: Genomic Analyses and Management of Agricultural and Industrial Microbial Genetic Resources and Associated Information

Location: Mycotoxin Prevention and Applied Microbiology Research

Title: A phylogenomic view of the Fusarium oxysporum Species Complex provides a robust framework for addressing questions in systematics, ecology and plant pathology

item GEISER, DAVID - Pennsylvania State University
item PARK, BONGSOO - Pennsylvania State University
item KANG, SEOGCHAN - Pennsylvania State University
item LAGOZE, LUCY - Pennsylvania State University
item WALLACE, EMMA - Pennsylvania State University
item JIMENEZ-GASCO, MARIA DEL MAR - Pennsylvania State University
item DEMERS, JILL - Pennsylvania State University
item O`Donnell, Kerry
item Burkhardt, Alyssa
item Martin, Frank
item FOKKENS, LIKE - University Of Amsterdam
item REP, MARTIJN - University Of Amsterdam

Submitted to: Meeting Abstract
Publication Type: Abstract Only
Publication Acceptance Date: 7/21/2018
Publication Date: 7/21/2018
Citation: Geiser, D., Park, B., Kang, S., Lagoze, L., Wallace, E., Jimenez-Gasco, M., Demers, J., O'Donnell, K., Burkhardt, A.K., Martin, F.N., Fokkens, L., Rep, M. 2018. A phylogenomic view of the Fusarium oxysporum Species Complex provides a robust framework for addressing questions in systematics, ecology and plant pathology [abstract].

Interpretive Summary:

Technical Abstract: Members of the Fusarium oxysporum species complex (FOSC) cause devastating vascular wilt diseases on a broad array of crop plants. In addition, some FOSC are known to inhabit soils and plants as presumed non-pathogens, and others inhabit plumbing systems and are associated with serious human infections. Initial attempts to produce a comprehensive phylogeny of the FOSC were hindered by a lack of concordance between phylogenies inferred from different loci. With the goal of producing a highly resolved phylogeny, we used a phylogenomic approach to extract 41 highly informative orthologous protein-coding genes useful for inferring organismal history in this group. OrthoMCL was used to identify orthologous protein clusters from the genomes of the FOSC, F graminearum, F. verticillioides, and an undescribed species in the F. solani Species Complex (FSSC 11). From the initial set of 9037 orthologue clusters identified, 4056 were found to represent a single protein from each of the four Fusarium genomes. Of these 4056 putative single-copy orthologues, only one mapped to a “lineage-specific” chromosome previously identified in the FOSC, with three additional loci mapping to unassembled contigs. This is hypothesized to reflect a strong connection between gene orthology patterns and the core genome of the FOSC. The coding sequences of each putative orthologue were then extracted from ten additional FOSC genomes and subjected to neighbor-joining bootstrap analysis, as a simple means to assess phylogenetic signal. 41 loci that provided =70% bootstrap support at seven or more nodes in the phylogeny of the eleven FOSC were then extracted from complete genome sequences of >100 FOSC isolates. Resulting sequences, covering 69,201 nucleotide sites with 9,479 parsimony-informative characters, were aligned and subjected to a phylogenetic analysis. The resulting tree showed highly supported terminal clades, providing evidence for species boundaries within the FOSC, along with signatures of historical recombination within terminal species lineages. In addition, relationships between pathogenic and non-pathogenic isolates within clades suggest possible models for acquisition and loss of pathogenicity determinants. This highly resolved view of the evolution of the FOSC based on its core genome provides a powerful vantage point for observing the evolutionary patterns associated with pathogenicity and niche adaptation in this extremely important group of fungi.