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theses

Xylella fastidiosa is broad-host-range plant pathogen responsible for significant commodity crop damage in much of the Western Hemisphere. Since its description in 1892, focus has centered around disease associated with Vitis (grape) hosts. Shade tree host studies of X. fastidiosa populations, however, have been both sparse and regionally oriented, making the exploration of infected oak stands an important area for greater understanding of this phytopathogen. To describe novel genetic profiles of the oak associated pathogen, Northeastern and Mid-Atlantic populations were assessed both phylogenetically and with Principal Component Analyses (PCA) and Minimum Spanning Trees (MSN). Polymerase chain reaction (PCR) based locus recoveries identified previously undescribed genetic diversity and phylogenetically separated oak associated populations based on host geography. Expanded analysis of insertion/deletion regions associated with the oak pathogen was also conducted for fine separation of populations relative to phylogenetic recoveries. Together these provided an efficient means to track the spread of the pathogen at the population level. To further explore genetic diversity in understudied X. fastidiosa oak populations, the genome of a Northeastern Quercus palustris associated X. fastidiosa isolate, RNB1, was sequenced and analyzed. Existing isolate comparisons described several novel RNB1 genomic regions, including two potential vir genes, and a Gene Ontology procyclic repeat pathogenesis locus. This work provided the first comparative look at an oak associated X. fastidiosa genome and described its composition relative to well described isolates. A final search for novel population specific markers in X. fastidiosa colonies targeted prophage segments. Thirteen regions across nineteen genomes were qualitatively described, with phage repressor and terminase suggestive of previously confirmed phylogenetic relatedness at an integrated phage-based locus. This data was then used in several machine learning approaches and proved accurate in predicting taxonomic categories across disparate X. fastidiosa populations when trained with matrix transforms of host specific X. fastidiosa prophage regions. This final study described evolutionary significance of widely profiled prophage regions and introduced an algorithmic approach for future large-scale genetically themed X. fastidiosa based population studies. Overall, the work herein presents previously undescribed genetic aspects of oak associated X. fastidiosa populations and posits a novel method for future data synthesis.

ETD_6794

Ph.D.

Includes bibliographical references

by Gregory Behringer

doi:10.7282/T3V126R9

ETD doctoral

The author owns the copyright to this work.