Date of Award


Document Type


Degree Name

Master of Science (MS)


College of Science and Mathematics



Thesis Sponsor/Dissertation Chair/Project Chair

John J. Gaynor

Committee Member

Scott L. Kight

Committee Member

Lee H. Lee


The discovery of the mitochondrial DNA (mtDNA) in the early 1960’s ushered in the field of organellar genetics. Evidence from both genetic and physical techniques has demonstrated that mtDNA are generally circular in structure, and that they represent the vestigial structure of the ancestral prokaryotic endosymbiont genome (Nosek et al., 1998). The more than 90 vertebrates and invertebrates sequenced to date have been found to have a remarkably constant gene content. With few exceptions, each contains the genes for 13 energy pathway proteins, the 2 RNA components of mitochondrial ribosomes (23S and 16S rRNA), and 22 transfer RNAs (Pont-Kingdon et al., 2000).

Biologists have long favored Hydra, a member of phylum Cnidaria, as a model organism for the study of development (Burnett, 1973). Because of its simple body plan, ease of culture, and clonal reproduction by somatic budding, it has found a unique niche in teaching and research laboratories (Lenhoff, 1983). A rather unusual feature in certain species of Hydra is that their mitochondrial genome is composed of two separate linear molecules of approximately 8.1 and 8.2 kb in length (Warrior and Gall, 1985; Warrior, 1987). Although the presence of linear genomes is rare, linear mtDNAs have been reported in a number of simpler eukaryotes such as Chlamydomonas, Paramecium, and Tetrahymena (Nosek et al., 1998).

In this study, we were interested in investigating how various strains and species of Hydra are related not at the morphological level, but rather at the molecular level using genes of the mitochondrion. While previous work has examined the relationship of the genome of two species of Hydra to other cnidarians, it was based on nuclear genes (Gauchat et al., 2000). Ribosomal DNA genes have proved very useful for assessing phylogenetic relationships (Hillis et a l, 1991). Therefore, our main focus of this project will be on the large-rRNA gene, however we will also sequence and analyze the gene for a tRNA, specifically tRNA-tryptophan (tRNA-Trp) along with cytochrome oxidase subunit two (COII), which is part of the terminal enzyme of the mitochondrial respiratory chain (Brunori et al., 2005)

These mitochondrial genes from a collection of Hydra were isolated, sequenced and analyzed. This was achieved by designing primers, amplifying via PCR, and sequencing these regions using an ABI 310 Prism Genetic Analyzer. The sequence data was analyzed via the ClustalX software program. From this information a tree building method was employed to generate phylogenetic trees, which is a graphical representation of evolutionary relationships. These trees allowed for the inference of how our collection of Hydra species and strains are related to each other at the molecular level.

This project inferred that the Hydra viridissima was the most distantly related Hydra within our collection, followed by the Hydra littoralis. The rest of the Hydra within our collection were divided into two groups. One group was composed of Hydra vulgaris (strain Japan), Hydra attenuata and Hydra vulgaris (strain Basel) obtained by Dr. Kass. The other group was comprised of Hydra vulgaris (strain AEP), Hydra magnipapillata, and Hydra vulgaris (strain Basel) obtained by Dr. Bode.

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