Phylogenetic models, distribution, and evolution of retroids.

Genetic elements that encode reverse transcriptase (RT) are called retroids. The abundance of retroids suggests they are important element of many genomes. Retroviral and other reverse transcriptase (RT)-containing retroids are subject to unique evolutionary pressures. A new maximum likelihood amino acid substitution matrix, rtREV, is developed for phylogenetic analysis of RT, and shown to perform better on a range of retroid datasets. While retroids are numerous in Eukarya and have been identified in some Eubacteria, assessing their presence in the third division of life, Archaea, is important to addressing whether they date back to the cenancestor. Several retroids from the complete genomes of the archaeans Methanosarcina acetivorans and M. mazei are characterized. Phylogenetic analysis with rtREV indicates several lateral gene transfers of these retrointrons and retrons from Eubacteria to Archaea, indicating they are recent additions to Archaea. Eukaryotes require telomerase for maintenance of the chromosome ends, and the relative ancestry of telomerase and other eukaryotic and eubacterial retroids is of interest. To address this question, seven conserved domains in diverse retroids and RNA-dependent RNA polymerases (RDRPs) were detected and aligned. Phylogenetic analyses of these domains without RDRP, rooted with eubacterial retoids, suggests that telomerase is ancestral to the other eukaryotic retroids. However, the observation that retroids from Archaea, Eukarya and Eubacteria are not reciprocally monophyletic suggests that eubacterial retroids do not form a proper outgroup. Alternatively, when rooted with an RDRP outgroup, telomerase is monophyletic with bacterial retroids. This incongruence between the origin of telomerase and other eukaryotic retroids suggests that other retroids may have maintained linear chromosomes, as is the case with the TART-A retroposon in Drosophila melanogaster.Ph.D.Biological SciencesBiophysicsMolecular biologyUniversity of Michigan, Horace H. Rackham School of Graduate Studieshttp://deepblue.lib.umich.edu/bitstream/2027.42/124303/2/3137932.pd