A Bioinformatics Pipeline To Study The Dynamics Of Retrotransposons In Grass Evolution

ASU Author/Contributor (non-ASU co-authors, if there are any, appear on document)
Andrew E. Murray (Creator)
Institution
Appalachian State University (ASU )
Web Site: http://www.library.appstate.edu/
Advisor
Matt Estep

Abstract: Transposable elements (TEs) are repetitive sequences found within all eukaryotic genomes and possess the genetic mechanisms necessary to move locations within their host. The repetitive fraction of plant genomes has historically been viewed as “junk DNA”. A growing body of evidencesuggests that repetitive sequences play a large role in the evolution of species and may influence diversification rates. Using bioinformatic approaches we mined nine million, 250 base pair illumina reads from four grass species closely related to maize (Zea mays) and have identified 121 Long Terminal Repeat-Retrotransposons (LTR-RTs). These include TE’spreviously identified in maize (3) and novel LTR-RTs (118) using the 80:80:80 homology rules for identification. Using these identified TE’swe are able to calculate the abundance of each element within the sampled grass genomes and using a phylogenetic framework, map changes in copy number to examine the dynamics of LTR-RTs proliferation and extinction within the grass lineages. Using this bioinformatic approach we can begin to examine the complex relationship between grass diversification and theproliferation of the TEs contained within their genomes.

Additional Information

Publication
Honors Project
Murray, A. (2017). "A Bioinformatics Pipeline To Study The Dynamics Of Retrotransposons In Grass Evolution." Unpublished Honors Thesis. Appalachian State University, Boone, NC.
Language: English
Date: 2017
Keywords
Retrotransposon, Bioinformatics, Long Terminal Repeat, Annotation Pipeline, Maize

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