Document Type

Thesis

Date of Award

5-19-2010

School/College

College of Science, Engineering, and Technology (COSET)

Degree Name

MS in Biology

First Advisor

Hector Miranda

Abstract

Microorganisms are hypothesized to experience rapid rates of mutation in space due to microgravity and ionizing radiation. As an initial effort to test the relative rates to which certain genes evolve under space-like conditions, we reviewed the usefulness and reliability of mitochondrial cytochrome oxidase 1 (Cal) gene in resolving the evolutionary relationships of Aspergillus and related fungi. The objectives of this study are to 1) characterize the mitochondrial Cal gene of Aspergillus and related fungi, 2) align the homologous sequences of Cal genes across the selected taxa, and 3) conduct phylogenetic analysis using parsimony, distance methods, and maximum likelihood. Most recently, the 600 bp region of the 5'end of the Cal gene was proposed to be the ideal marker for barcoding eukaryotes. However, several investigators have suggested potential problems associated with the use of Cal gene as a universal marker for fungi. Of those, they include failure to resolve closely related taxa and extensive overlap of 1 intra- and interspecific diversity. The universality of the gene is also questioned by reports of the prevalence of mobile introns across many fungal groups. We investigated the utility of COl gene in discrimination between species, between strains and between geographic isolates. We sequenced 5 species from ATCC, plus an unknown culture obtained from environmental samples. For the analyses, alignments were done using Geneious Pro (Biomatters, Ltd., New Zealand). Final alignments were exported in nexus file format. Using PAUP©4blO, we conducted phylogenetic analyses thru Maximum Parsimony (MP), distance method using Neighbor-Joining, and Maximum Likelihood (ML). Support for nodes were estimated using nonparametric bootstrap and were done for MP, distance and ML analyses. The substitution model of molecular evolution used was Jukes-Cantor. Our preliminary analysis suggested the following observations. 1) The conflict in the utility of COl as barcoding marker reflects the lack of taxonomic stability within Fungi at the intra- and inter- species level. There is a need to expand geographic sampling of taxon to further test the validity of current classification. 2) No intron was observed within the short barcode region (600 bp) among the samples we investigated.

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