Undergraduate Honors Thesis Projects

Date of Award

Spring 5-3-2026

Document Type

Honors Paper

Degree Name

Biochemistry and Molecular Biology-BS

Department

Biochemistry and Molecular Biology

Advisor

Dr. Brandon Sinn

First Committee Member

Dr. Ann Feke

Second Committee Member

Dr. John Tansey

Keywords

Evolution, Transcriptome, DNA Mismatch Repair, Mychoheterotroph; Orchids

Subject Categories

Bioinformatics | Botany | Evolution | Genomics | Higher Education | Molecular Biology | Molecular Genetics | Plant Breeding and Genetics

Abstract

All orchids are mycoheterotrophs early in development, parasitizing fungi to acquire nutrients during germination. While most orchids transition to autotrophy as they mature, others have lost the ability to photosynthesize and continue to parasitize fungi. The genus Corallorhiza is of particular interest as it is comprised solely of early-transitional species amongst which a gradient of reduction exists for chlorophyll production and plastome length, gene content, and photosynthetic machinery. Corallorhiza species provide an opportunity to observe changes in gene regulation, particularly those implicated in repair pathways, that might underlie the shift in trophic mode and concurrent genome instability that has been characterized in the group. DNA Mismatch Repair (MMR) is a pathway of interest as it functions to maintain genomic stability and correct mutations. Here, we describe the results of a phylotranscriptomic investigation of differential gene expression of MMR genes using four species comprising a gradient of genomic instability in Corallorhiza. Tests of differential expression were conducted separately for above and belowground tissues for two groups of comparison/contrasts consisting of pairs from later-versus early-mycoheterotrophic pairs of taxa: C. striata versus C. trifida; and C. striata, maculata, and wisteriana versus C. trifida. We found that all MMR subunit genes were present in the transcriptomes of each species, including evidence of paralogs. Multiple components of the Mismatch Repair Pathway, such as MLH1, RFC3, MSH6, PCNA, RPA2, and RPA70B, are downregulated in the aboveground tissues of later-stage mycoheterotrophs relative to the earliest-stage, while MSH1, MSH2, MSH3, and PCNA are upregulated in the belowground tissues. MSH5 and RFC1 are consistently upregulated across all tissues in late-stage mycoheterotrophs. This study is the first ever characterization of the MMR pathway in Corallorhiza orchids. It improves our understanding of the function and evolution of this pathway through the transition from earlier-to-later stage mycoheterotrophy in a genus of early-transitional mycoheterotrophic orchids.

Licensing Permission

Copyright, all rights reserved. Fair Use

Acknowledgement 1

1

Acknowledgement 2

1

Download

Available for download on Monday, April 15, 2030

Share

COinS