Semester

Summer

Date of Graduation

2013

Document Type

Dissertation

Degree Type

PhD

College

Davis College of Agriculture, Natural Resources and Design

Department

Biochemistry

Committee Chair

Stephen DiFazio.

Abstract

Whole genome duplication is a recurrent phenomenon throughout the history of flowering plants, with at least 1 occuring in the history of each angiosperm lineage. However, following duplication the genome typically undergoes a period of increased structural rearrangements and gene loss, resulting in a diploidized genome with large stretches of syntenic regions resulting from the duplication. This process, termed fractionation, often exhibits biased patterns of gene retention, which appear to correspond with the putative connectedness of genes within biological networks. In this thesis, I explore the extent to which the same biases appear in duplicate genes from the most recent whole genome duplication in Populus trichocarpa, how those biases relate to inferred network properties, and whether the ongoing process of nonfunctionalization within populations exhibits similar patterns to the historical trends. In Chapter 2, I compare the factors affecting retention of duplicates following both tandem and whole genome duplication. I show that these differ in a manner consistent with the action of a selective drive to maintain dosage balance. I also find that many duplicate pairs have more conserved expression patterns than expected by chance, consistent with the action of purifying selection for the maintenance of gene dosage. In Chapter 3, I use statistical learning to predict a protein-protein interaction network for P. trichocarpa and several model organisms. Using these predicted networks, I show that the probability of retention following several whole genome duplications in both P. trichocarpa and Arabdidopsis thaliana is positively related to the relative abundance of duplicated neighbors and that the effect is enhanced with higher connectedness, consistent with a drive to maintain dosage balance between well-connected duplicates within biological networks. In Chapter 4, I use next generation sequencing to define small and large deletions within natural populations of P. trichocarpa. The patterns of enrichment among the deletions putatively causing nonfunctionalization events parallel the biases observed in chapters 2 and 3. This research therefore supports the importance of dosage balance during the fractionation process and illustrates how the observed biases continue to arise within natural populations.

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