Doctor of Philosophy (PhD)


Plant Pathology and Crop Physiology

Document Type



Cercospora leaf blight (CLB) and purple seed stain (PSS) are common soybean diseases in the Gulf South of the United States (USA). For nearly a century, Cercospora kikuchii has been considered as the only pathogen causing these diseases. However, previous reports of genetic diversity among isolates collected throughout Louisiana suggested the presence of multiple lineages or species. Recent systematic studies classified species of Cercospora using a taxonomic system based on phylogenetic analysis of five nuclear loci (legacy genes). Using a similar approach, cercosporoid fungi tentatively identified as C. kikuchii were evaluated along with 53 other species of Cercospora. No isolates from this study were nested within the clade including the ex-type strain of C. kikuchii. Five isolates grouped with C. cf. sigesbeckiae and all others were part of C. cf. flagellaris. Several isolates of C. cf. flagellaris were also obtained from Gossypyium hirsutum and Phytolacca americana. These results suggest that C. kikuchii is not the organism responsible for causing CLB or PSS in the Gulf South and other areas of the USA. Multiple haplotypes were observed at each locus and individual genes varied in their resolving power. Most species were monophyletic in concatenated analyses, but reciprocal monophyly was generally not observed within individual gene trees. Furthermore, node support values were generally low across all topologies, indicating that the phylogenetic markers most commonly used for systematic studies of Cercospora are limited to answering shallow-level taxonomic questions. However, existing genome sequence data provided an excellent opportunity to develop new markers with stronger phylogenetic signal to better understand the evolutionary history of Cercospora. Sixty-three exon-flanked intergenic regions, syntenic between the genomes of C. cf sigesbeckiae and C. canescens, were extracted and aligned, then ranked and filtered according to several metrics to assess their phylogenetic utility. Candidate markers were validated by PCR on 24 Cercospora species, including 16 type strains. Assessment of phylogenetic informativeness profiles and phylogenetic analyses showed that all of the new markers provide greater interspecific resolution than the legacy genes and offer new options for identifying cryptic species in complex clades like C. cf. flagellaris.



Document Availability at the Time of Submission

Student has submitted appropriate documentation to restrict access to LSU for 365 days after which the document will be released for worldwide access.

Committee Chair

Schneider, Raymond