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Date of Graduation
5-9-2024
Semester of Graduation
Spring
Degree Name
Master of Science (MS)
Department
Department of Biology
Second Advisor
Alfredo López-Caamal
Third Advisor
Raymond Enke
Fourth Advisor
James Herrick
Abstract
Cytonuclear incompatibilities are proposed to be one of the first genetic barriers to arise during speciation, so understanding the underlying evolutionary forces that contribute to cytonuclear incompatibilities is important. Many studies have looked at SNP level variation in the plastid genome and its relationship with cytonuclear incompatibility, but no studies have examined structural variation and its relationship to cytonuclear incompatibility, particularly at the early stages of speciation, i.e. within species. Campanula americana is a great system for this because it exhibits cytonuclear incompatibility and the family in which it is found, the Campanulaceae, exhibits rapidly evolving plastid genomes, including elevated levels of nucleotide substitution in some plastid genes, large levels of repetitive DNA and structural rearrangements. However, characterizing structural variation (SV) in the plastid genome requires de-novo assembly of plastid genomes from multiple lineages, and assembling complex genomes can be difficult. We developed a bioinformatics pipeline for assembly of complex plastid genomes to characterize structural variation within C. americana, but also to develop a novel CURE-like module centered around Nanopore’s MinION sequencer to bring genomics and bioinformatics to the classroom, exposing students to cutting edge genomic technologies and bioinformatics techniques. We overall found no large-scale structural variation within C. americana, which leads to the conclusion that SV is likely not contributing to cytonuclear incompatibility within C. americana. We did find the Appalachian plastid genome contained a larger percentage of tandem repeats than the other two, which may be related to the incompatibility between lineages. On the classroom side, students that had the sequencer present during the duration of the module reported a more significant impact of the module in terms of positive responses than students who didn’t have the sequencer present. This impact seems to stem from students' confidence to perform sequencing and explain the entire genome assembly process from DNA extraction to bioinformatic analysis. Lastly, we found that specific sets of students, such as first-generation students or biology/biotech majors, appear to have experienced a greater impact from being able to physically interact with the MinION sequencer than other students.
