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A DISSERTATION Presented to the Faculty of The Graduate College at the University of Nebraska In Partial Fulfillment of Requirements For the Degree of Doctor of Philosophy. Copyright 2006 Lisa Fitzgerald.


The family Phycodnaviridae consists of a morphologically similar but genetically diverse group of large dsDNA viruses which infect both fresh and marine water eukaryotic algae. Two viruses, the 370 kb Chlorella NC64A virus NY-2A and the 313 kb Chlorella Pbi virus MT325, from the family Phycodnaviridae, genus Chlorovirus, were sequenced, analyzed, and compared to the prototype chlorella virus PBCV-1. The NY-2A genome, the largest chlorella viral genome sequenced to date, contains 886 open reading frames (ORFs) of 65 codons or larger and encodes 404 putative proteins and 7 tRNAs. The MT325 genome, the smallest chlorella viral genome sequenced to date, contains 845 ORFs and encodes 331 putative proteins and 10 tRNAs. The protein-encoding genes are evenly distributed on both strands, and the intergenic space is minimal. Approximately 50% of the viral gene products have been identified, including some which are the first of their type to be detected in a virus. Domain scatter plots revealed that NY-2A and MT325 are mosaics of both prokaryotic- and eukaryotic-like proteins. A comparison of the three chlorella viruses sequenced, NY-2A, MT325, and the previously sequenced PBCV-1, revealed that ~75% of the viral encoded proteins are homolgous. However, 64% of these homologs are classified as unknowns based on a lack of sequence similarity to proteins in public databases. In addition to the genomic annotations, I conducted an extensive comparison of the chloroviruses to other phycodnavirus members as well as other large dsDNA viruses. Surprisingly, only 10 (~3%) of the chlorovirus genes are encoded by all six of the sequenced phycodnaviruses. Adviser: James L. Van Etten

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