Date of Award


Document Type


Degree Name

Master of Science (MS)


College of Science and Mathematics



Thesis Sponsor/Dissertation Chair/Project Chair

Charles Du

Committee Member

John Gaynor

Committee Member

Carlos Molina


Long terminal repeats (LTR) retrotransposons, found across eukaryotes, are transposable elements which can copy and insert themselves into other loci within a genome. These transposable elements are similar to retroviruses in that they rely on reverse transcriptase to “copy and paste” themselves elsewhere in the genome. From the RNA transcript they are able to use reverse transcriptase to make another DNA copy of themselves. This initially gave them the moniker, selfish genes. However, in the decades after the discovery of reverse transcriptase and LTR retrotransposons, it became known that non-genic DNA could have other functions. LTR retrotransposons are sources of mutation, inserting themselves into and mutating genes within their host organism. However, LTR retrotransposons are prone to mutation themselves, quickly becoming inactive, incapable of transposition. LTR retrotransposons constitute approximately 75% of the total genomic sequence of maize. The vast majority of these LTR retrotransposons are completely inactive. While these inactive retrotransposons can be useful for gleaning information about an organism’s evolutionary history, the active LTR retrotransposons are of more interest. They are capable of causing mutations in current maize crosses and maize lines. In this study we created a tool that is adept at filtering out the inactive LTR retrotransposons and finding the location and sequence of potentially active LTR retrotransposons. Building off the freely accessible tool for locating LTR’s, known as “LtrDetector”, we added additional functionality. In an initial filter, LtrDetector found over three million potential LTR retrotransposons across thirty publicly available maize lines. After adding restrictions for size, an intact primary binding site, polypurine tract, reverse transcriptase, RNase and integrase we narrowed down that large pool of candidates to just twenty-seven potentially active LTR retrotransposons.

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Biology Commons