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Author ORCID Identifier


Campus-Only Access for Five (5) Years

Document Type


Degree Name

Doctor of Philosophy (PhD)

Degree Program

Organismic and Evolutionary Biology

Year Degree Awarded


Month Degree Awarded


First Advisor

Li-Jun Ma

Second Advisor

Laura A. Katz

Third Advisor

Michael Hood

Fourth Advisor

Adam H. Porter

Subject Categories

Bioinformatics | Computational Biology | Evolution | Genetics | Genomics | Other Immunology and Infectious Disease | Pathogenic Microbiology | Plant Pathology | Population Biology


Fusarium oxysporum is an economically important cross-kingdom fungal species. Members within this species complex not only cause Fusarium vascular wilt disease in over 100 plant species, but also infect human causing fusariosis. It is well documented that plant pathogenic F. oxysporum isolates are highly host-specific. A single pathogenic form usually infects a single or closely related plant species due to the presence of a distinct set of lineage-specific (LS) chromosomes in the genome. This dissertation investigated: 1) the presence and potential function of LS chromosomes in human pathogenic isolates; 2) the evolution and diversity of F. oxysporum f.sp. cubense (Foc), a group of pathogenic strains that have infected bananas over more than half century banana plantation history. Comparative genomics is employed to study the genomic dynamics of the compartmentalized F. oxysporum genomes; 3) transcriptomes of two different virulent Foc strains inoculating the same host were analyzed to characterize Foc infection process and to identify pathogenic factors involved in disease development and host response factors involved in the development of resistance. My work shows that a F. oxysporum clinical strain isolated from the blood of a fusariosis patient has a unique set of LS chromosomes. Functional analysis of these chromosomes indicates that they may contribute to the fungal adaptation to human body conditions, such as alkaline pH and limited metal ion environment. Interestingly, I do not find LS chromosomes in Foc strains, but they have LS sequences located at extended regions of core chromosomes. Comparative population genomic study of Foc suggested the monophyletic origin of Foc race4. Moreover, population structure analysis reveals that Foc isolates are highly diverse and can be grouped into three distinct phylogenetic populations. Finally, I characterize Foc infection process with two different virulent isolates race1 and TR4. I found that early time point is important for Foc infection. Plant host inoculated with more virulent strain TR4 displays weaker defense response. Meanwhile, TR4 nitrate/nitrite-dependent nitric oxide biosynthesis pathway is highly expressed, suggesting that nitric oxide is an important molecular mediating disease development.


Creative Commons License

Creative Commons Attribution-Noncommercial-No Derivative Works 4.0 License
This work is licensed under a Creative Commons Attribution-Noncommercial-No Derivative Works 4.0 License.