Date of Award


Document Type

Distinction Paper

Degree Name

Biochemistry and Molecular Biology-BS


Biochemistry and Molecular Biology


Dr. Brandon T. Sinn

First Committee Member

Dr. Jeffrey S. Lehman

Second Committee Member

Dr. Robin E. Grote


Whirly Transcription Factor, Mycoheterotrophy, Transcriptomics, Alternative Splicing, Nonsynonymous Substitutions, Phylogenetics

Subject Categories

Bioinformatics | Computational Biology | Evolution | Genetics | Genomics | Molecular Genetics


Mycoheterotrophy, or reliance upon fungi as an energy source, is common to all orchids at some point in their development. Species that do not conduct photosynthesis and instead parasitize fungi as their only carbon-based nutrition source are known as full mycoheterotrophs. While gene loss in the plastid and nuclear genomes due to relaxed selective pressures on photosynthetic function are well studied in mycoheterotrophs, the evolution of the molecular mechanisms controlling genome stability are completely unknown. Here I use a phylo-comparative approach to characterize the evolution of Whirly1 (WHY1), a transcription factor implicated in plastid genome stability and fungal defense, in the mycoheterotrophic orchid genus Corallorhiza. Together, the four species studied, C. trifida, C. striata, C. wisteriana, and C. maculata, represent a trophic gradient from partial to full mycoheterotrophy. I hypothesized that WHY1 was a single copy gene in these four Corallorhiza species and would be alternatively spliced and differentially expressed in aboveground inflorescence tissues and belowground rhizome tissues where the fungal host is found. This project used previously generated RNA-seq data to assemble de novo transcriptomes of each Corallorhiza species, identify WHY1 transcripts and any non-canonical transcripts, and investigate differential expression of these transcripts in both aboveground and belowground tissues. Additionally, sampling of WHY1 across angiosperms from public databases was conducted to provide phylogenetic context for the evolution of WHY1 in Orchidaceae, including Corallorhiza and two distantly related species of fully mycoheterotrophic orchids. Screening of the WHY1 sequence alignment of these taxonomic groups resulted in the identification of nonsynonymous substitutions specific to Corallorhiza, and those that potentially affect structure and function are discussed. In addition, Oxford Nanopore sequencing of Corallorhiza WHY1 genomic sequences provided supporting evidence for intron retention as part of the alternative splicing among the transcripts. Additionally, tests of selection regime at the gene and codon level revealed relaxation of purifying selection on WHY1 in mycoheterotrophic orchids, but this signal appeared to be driven by late stage fully mycoheterotrophic species. Overall, the results of this project suggest that pathway alteration of WHY1 precedes the establishment of potentially deleterious substitutions and reveal that splicing alteration and decreased expression of WHY1 are coincidental with the shift to full mycoheterotrophy.

Available for download on Tuesday, April 16, 2024