Undergraduate Thesis Or Project
 

Campbell final ThesisAutomated annotation of Caenorhabditis mitochondrial genomes and phylogenetic analysis.pdf

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https://ir.library.oregonstate.edu/concern/undergraduate_thesis_or_projects/5712m833b

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  • Abstract Motivation Relatively little is known about the evolution of mitochondrial genomes between Caenorhabditis species despite decades of research. Both the worldwide search for new nematode species and the effort to increase sequencing speeds require automated tools to quickly characterize and categorize large amounts of data. Results We developed an automated annotation tool for nematode mitochondrial genome sequences that characterizes individual genes in addition to pseudogenic and intergenic regions. The automated annotation tool utilizes the ClustalW multiple sequence alignment program to produce gene alignments of input genomic sequence versus literature C. elegans mitochondrial genes. A phylogenetic analysis was conducted by using RAxML 7.2.6 to create a maximum-likelihood tree with bootstrap analysis for 84 mitochondrial genomic sequences representing 23 Caenorhabditis species and 1 outgroup. Conclusion The automated annotation tool for Caenorhabditis mitochondrial genome sequences is fast and effective. The phylogram resulting from phylogenetic analysis provided preliminary insights into the evolutionary relationships among several Caenorhabditis species' mitochondrial genomes.
  • Keywords: phylogenetic, Caenorhabditis, mitochondrial genome, automated annotation
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