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Assessment of accessory genome and host-specific virulence in Fusarium




Pokhrel, Ambika

Type of Degree

PhD Dissertation


Entomology and Plant Pathology

Restriction Status


Restriction Type

Auburn University Users

Date Available



Members of the Fusarium solani and Fusarium oxysporum species complexes (FSSC and FOSC, respectively) comprise soil borne filamentous fungi of clinical and agricultural importance. The main focus of this study is to study the accessory genome and host-specific virulence factors in two members of the FOSC, Fusarium oxysporum f. sp. vasinfectum (Fov) and Fusarium oxysporum f. sp. pisi (Fop), and a member of the FSSC, Fusarium vanettenii (Fv) (previously known as Nectria haematococca MP VI and Fusarium solani f. sp. pisi). Both Fv and Fop are known to cause Fusarium root rot disease on garden pea (Pisum sativum L.), whereas Fov is known to cause Fusarium wilt disease on cotton (Gossypium sp.). The first research chapter of this study explores the virulence factors adopted by Fov during infection and colonization of cotton plants using a transcriptomic approach. This study revealed several genes encoding a multitude of different protein classes were upregulated after gossypol (antimicrobial compound or phytoalexin produced by cotton) treatment in Fov. Particularly the role of a gene encoding a lactamase domain LAC1 was explored for its role in virulence and gossypol tolerance. Detailed study of LAC1 found that it is a host specific virulence factor located in the accessory genome of Fov and is phylogenetically closer to a lactamase encoding gene from Verticillium dahliae (another soilborne cotton pathogen). In addition, using a metabolomic approach we identified potential substrates of Lac1 in cotton plants during infection. The second research chapter of this study is focused on the comparative genomic analysis and assessment of the accessory genome of the members of the FSSC and FOSC. The comparison of accessory scaffolds and PDA1 scaffolds of FSSC isolates revealed only a few syntenic regions between them and multiple rearrangements indicating a dynamic nature of these chromosomes and could serve as a hotspot for recombination. The synteny analysis of the PEP genes (PEP1, PEP2, cDNA3, PDA1, and PEP5) revealed that the PEP cluster is conserved only in the pea pathogenic FSSC isolates with PEP2, PDA1, and PEP5 being the most conserved genes in the cluster and is hypothesized to represent the ancestral organization of the cluster. In addition, from the genome analysis we were able to identify several secondary metabolite clusters and secreted proteins in FOSC and FSSC isolates that could be involved in virulence. The third research chapter of this study is focused on characterization of the gene cDNA3 from the PEP cluster in Fv. cDNA3 from Fv was particularly interesting because of its unknown function and presence only in the highly virulent field isolates. The biological function of cDNA3 was investigated using a mutational approach. Virulence, gene expression, and fluorescence microscopy studies identified that cDNA3 is a transcriptional activator of PEP genes and contributes to virulence towards garden pea. In conclusion, from this research on FOSC and FSSC members, we were able to explore the biological function of genes located in the accessory genome, LAC1 and cDNA3 and their role in fungal virulence and host-specificity. The comparative analysis of the accessory genomes of FSSC and FOSC identified that it may function as a hotspot for recombination and horizontal gene transfer, influencing or dictating the host range of these pathogens. Besides broadening our knowledge on accessory genome and its role in virulence and host-specificity, our research findings share potential for disease management and crop improvement.