Honors College Thesis
 

Exploring phylogeny of Rhodococcus fascians isolates using 16S ribosomal DNA sequence analysis

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  • Rhodococcus fascians is a Gram-positive, pleiomorphic actinomycete that causes leafy gall formation in a wide range of plant hosts. This particular phytopathogen has been a focus of research at the Oregon State University Plant Clinic, a diagnostic laboratory. Phylogeny of R. fascians isolates obtained from Plant Clinic submissions was determined with 16S ribosomal DNA (16S rDNA) sequence analysis with sequence primers designed to amplify specific regions of R. fascians 16S rDNA. A preliminary set of 21 Plant Clinic isolates was sequenced at the USDA/ARS Floral and Nursery Plants Research Unit in Beltsville, MD. Partial 16S rDNA sequences from the preliminary analysis were used to identify related database sequences of R. fascians isolated from non-plant environments with a nucleotide blast algorithm through the National Center for Biotechnology Information (NCBI). Phylogenetic analysis contained 84 R. fascians rDNA sequences; 70 Plant Clinic isolates, 14 related database isolates, and an outgroup of Proteobacteria. Three phylogenetic clades were identified according to most related database isolates: the Microbacteriaceae, CAGY6, and deep-sea actinomycetes. The 70 identified Plant Clinic isolates colonized a wide range of hosts including 21 different plant genera, and phylogeny was not dependent on the host species.
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