Master's Theses or Doctor of Nursing Practice

Department

Biology

Degree Name

Master of Science (MS)

Abstract

Harmful cyanobacterial blooms are a danger to freshwater systems, particularly in water limited regions such as western Kansas, yet the genetic identity and diversity of bloom-forming taxa in this region remain poorly characterized. In this study, I investigated a cyanobacterial bloom in Horsethief Reservoir (Kansas, USA) in summer 2024 with the aim of resolving the taxonomic identity and genomic features of the dominant organism. Bloom water samples were collected, and the dominant cyanobacterium was enriched and rendered nearly axenic through controlled cultivation and repeated subculturing. Preliminary 16S rRNA gene sequencing indicated affiliation with the genus Limnothrix, but with notable divergence from previously described strains. To achieve high-resolution genomic characterization, I implemented a hybrid whole-genome sequencing and assembly workflow integrating Illumina short-read and Oxford Nanopore long read data. Sequencing reads were quality-filtered and assembled using complementary hybrid assembly strategies, followed by annotation and rigorous quality assessment through k-mer–based consensus evaluation and coverage analysis. This approach yielded a high-quality, complete genome assembly with no detectable consensus errors and strong support from read-backed validation. The hybrid strategy enabled accurate resolution of repetitive regions and structural features that are typically difficult to reconstruct using single-platform sequencing approaches. Comparative genomic and structural analyses revealed both conserved and novel genetic features relative to the only available reference genome, including multiple large-scale genomic inversions that indicate substantial structural divergence and support the classification of this isolate as a distinct lineage. Functional annotation identified genes associated with key metabolic and ecological processes relevant to bloom formation. Collectively, this study demonstrates the effectiveness of hybrid genome assembly for resolving complex cyanobacterial genomes and provides one of the first genome-resolved insights into bloom-forming cyanobacteria in western Kansas, thereby advancing our current understanding of their diversity and ecological significance in freshwater systems.

Keywords

Genome rearrangements, Water resource management, Blue-green algae, Environmental genomics, Drinking water safety

Advisor

Dr. Michael Gruenstaeudl

Date of Award

Spring 2026

Document Type

Thesis

Rights

© The Author

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