Chemistry, Department of
Department of Chemistry: Dissertations, Theses, and Student Research
Date of this Version
3-30-2006
Document Type
Dissertation
Citation
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
Major: Chemistry
Lincoln, Nebraska, March 30, 2006
Abstract
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
Comments
Copyright 2006, Lisa Fitzgerald. Used by permission