| Transposable elements (TEs) are self-replicating genetic elements that comprise a large portion of all characterized nuclear genomes. Self-replication, which is catalyzed by proteins encoded by autonomous TEs, permits TEs to persist without necessarily providing immediate adaptive benefit to the organism; therefore, TEs are sometimes characterized as selfish, parasitic, or junk DNA. Nevertheless, over the course of evolution, TEs have produced diverse and vital eukaryotic adaptations. One way in which TEs coevolve with ordinary genes is by direct sequence exchange: TEs can duplicate and mobilize ordinary genes; conversely, TE-derived sequences can become conserved as ordinary genes. In this thesis, I use genome-scale bioinformatic analyses to identify direct sequence exchanges from plant genomes to TEs, and vice versa, and to characterize their functional and evolutionary consequences. After reviewing the literature, I first examine Mutator-like elements (MULEs) in rice that have duplicated and mobilized thousands of ordinary coding gene fragments, a process we term transduplication. Contrary to a previous report, these sequences do not appear to produce functional proteins, although they may have regulatory functions. Second, I examine a gene family that appears to have originated through transduplication in Arabidopsis thaliana MULEs, which is conserved within TEs, called Kaonashi (KI). KI shows that transduplication does occasionally produce functional gene duplications; however, at least in this case, the result is a not a new ordinary gene, but a new TE gene. Finally, I examine ordinary genes in A. thaliana derived from TE genes, a process termed molecular domestication. In addition to 3 previously known A. thaliana domesticated transposable elements (DTEs) families, I identify 23 candidate novel families. Together, these results support the view that, despite persisting by self-replication, TEs are not molecular parasites but are integral components of eukaryotic genomes. |
