Mitochondrial Genomes as Tools for Analysis and Teaching of Comparative Genomics, Evolution, and Ecology

Pogoda, Cloe Simone

Graduate Thesis Or Dissertation

Mitochondrial Genomes as Tools for Analysis and Teaching of Comparative Genomics, Evolution, and Ecology Public Deposited

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Citeable URL: https://scholar.colorado.edu/concern/graduate_thesis_or_dissertations/9c67wm901

Abstract

Mitochondria produce ATP, the energy molecule necessary for the biosynthetic pathways of life. They are thought to be one of the first landmark symbiotic events; having originated through endosymbiosis of an early alphaproteobacterium into a host cell. The mitochondrial genome has undergone significant changes in organization, size and complexity due to loss of protein coding genes. However, this complexity can vary widely between the major eukaryotic domains of life, with some mitochondria streamlined to less than 1% of the original genome size, particularly in metazoans, while plants and fungi show much larger, less streamlined mitochondrial genomes. Nevertheless, all mitochondrial genomes are small in comparison to the nuclear genome, and are present in high copy number and uniparentally inherited. Embedded in the double membrane of the organelle are five protein complexes that work together to produce ATP. These unique genome features contribute to make the mitochondria a powerful genetic tool for studying broad ecological and evolutionary questions among myriad of species. This thesis interrogates the mitochondrial gene content, exon-intron structure, organization and ancestral states of pertinent genome features for two biologically important species: lichens and diatoms. Lichens are an obligate symbiosis ideal for exploring the genomic consequences of resource sharing involved in a mutualistic relationship. They are estimated to cover up to ten percent of the earth’s landmass and contribute importantly to the process of carbon fixation and oxygen production. Diatoms are extremely successful unicellular, photosynthetic, eukaryotic algae that inhabit both freshwater and marine habitats. They have the most efficient RuBisCO enzyme recorded among autotrophs and marine diatoms alone are estimated to perform 20% of the global carbon fixation; an amount comparable to all terrestrial rainforests. These two species have been extensively studied using classical experimental techniques, but have a dearth of genetic resources available. To better understand these extremely important species I harnessed the mitochondrial genome to make comparisons across the lichen and diatom trees of life. In order to examine the genetic content of these mitochondrial genomes, I utilized many different bioinformatics tools. In concert with my own data collection, I helped design a course curriculum, and associated course materials, designed to teach upper level undergraduate and graduate students how to properly assemble and annotated mitochondrial genomes. My thesis not only demonstrates the utility of the mitochondrial genome for answering important evolutionary questions in diverse and important species, it also presents one method for teaching other researchers the tools necessary to assemble and annotate organellar genomes of interest for their own research.

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