Doctor of Philosophy (PhD)


Biological Sciences

Document Type



Comparative genomic analyses were performed to gain insights into the organization and content of the genome of Streptomyces ipomoeae, the soil rot pathogen that infects sweetpotatoes. Unlike Streptomyces scab pathogens, the thaxtomin phytotoxin gene cluster (txt) in S. ipomoeae does not appear to reside within a genomic island and has diverged from its scab pathogen counterparts. Increased usage of the rare TTA codon, particularly for the txt cluster, suggests greater translational control by the bldA tRNA in S. ipomoeae. Orthologous gene searches and secondary metabolite profiling yielded ortholog groups and metabolite gene clusters that were exclusive to S. ipomoeae, and which may contribute to the unique aspects of soil rot disease and/or to the ecological persistence of this pathogen.

The main management practice against soil rot is the breeding for resistant sweetpotato cultivars, which relies on laborious field tests. Therefore, the development of a more efficient, yet reliable method for evaluating resistance in a controlled in vitro environment could benefit breeding programs. Here, the roots of sterilely grown plantlets were inoculated with pathogenic S. ipomoeae, and disease onset and progression were then quantified under varying in vitro conditions. Overall, resistant cultivar 86-33 showed significantly greater resistance to disease than the susceptible cultivar Jewel in vitro when assays were conducted in soil. Based on results here, accurate resistance/susceptibility profiling may also be possible if plantlets are first exposed to soil and then transferred to agar plates for the remainder of the assay.

Finally, by combining available transcriptomic and genomic data involving the scab pathogen Streptomyces scabiei, we identified a pectate lyase gene, SCAB_44901, which may have a role in pathogenicity. To investigate this possibility, a targeted deletion mutant of S. scabiei (ΔSCAB_44901) was constructed. In a pathogenicity assay using radish seedlings, no differences in disease development between the wild type and the ΔSCAB_44901 mutant were observed, though S. scabiei codes for additional pectate lyases that could potentially compensate for the lack of SCAB_44901 protein in this mutant. The next step is to overexpress the SCAB_44901 gene in a heterologous non-pathogenic host to check for signs of virulence.



Committee Chair

Pettis, Gregg S.