Duvall, Melvin R.
Ph.D. (Doctor of Philosophy)
Department of Biological Sciences
Today, researchers are inundated with an overwhelming amount of data due to advances in DNA sequencing technologies. This has benefited the fields of both bioinformatics and phylogenomics substantially. With the ability to increase sampling at both the taxonomic and molecular levels, we are now able to produce robust phylogenomic reconstructions and better discern relationships between taxa.
The goals of this dissertation are in two distinct parts: 1) to advance the understanding of land plant terrestrialization and evolution through examination of the closest relative to the land plant lineage, a species of green algae; and 2) to explore evolution among a subfamily of grasses to gain insights into later evolution of the land plant lineage through genetic evidence of large and rare mutational events and calibrate fossil divergence estimates.
Both of my research aims use DNA sequence data, derived through next generation (NGS) and third generation (TGS) sequencing methods, which have increased accuracy and efficiency for sequencing DNA in high volumes. In particular, my first research project utilized Oxford Nanopore (TGS) sequencing to provide continuous long-read sequencing for use in assembly verification of the mitochondrial genome (mitogenome) and plastid genome (plastome). I sequenced and contributed to NCBI’s GenBank repository, the first mitogenome from Zygnema, and the plastome as well. Data representation in publically available repositories of the Charophyte algae is particularly sparse. Additionally, I catalogued and surveyed genes across the Chlorophyta, Charophyta, and Embryophyta, providing a pan-genome analysis of genes and gene functions most likely necessary for terrestrialization.
My second research project explored the grass subfamily Pooideae. Specifically, this project investigated the relationships between Group 1 and Group 2 chloroplast type species in the Poeae tribe utilizing NGS derived data. This peculiar relationship is only seen in chloroplast data, and my aim was to explore rare genomic changes (RGCs) as a potential explanation for this division between members of the tribe. I sequenced and contributed 16 Pooideae plastomes to NCBI’s GenBank data repository. Overall, I discovered the utility of RGCs as taxonomic markers.
My final project more broadly explored relationships among the Pooideae subfamily of grasses. In this study, I sequenced and contributed 47 new Pooideae plastomes to NCBI’s GenBank data repository, and I produced a dataset encompassing 313 complete plastomes from the grass family. Of the 313 plastomes, over half the data set (164) are Pooideae species. This is the largest complete plastome study to focus on pooid grasses. Additionally, I expanded my fossil calibration points for the divergence date analysis to include 14 accepted grass fossils and create a more accurate and robust picture of evolution in Poaceae as a whole. The dates returned in my analysis were in line with, but slightly older than the most recent estimates.
In analyzing DNA across all of my studies, computational methods (bioinformatics) are necessary to adequately process the vast amounts of data generated through these new sequencing technologies. Oftentimes, bioinformatic scientists must devise their own tools through computer programming, and are equally biologists and computer scientists. Ultimately, a bioinformatic approach to exploring land plant evolution provides computationally reinforced, robust analyses to explain the evolutionary histories of the land plant lineage.
Orton, Lauren Margaret, "A bioinformatic approach to exploring land plant evolution" (2020). Graduate Research Theses & Dissertations. 7511.
Northern Illinois University
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