Genomic PCR validation of InDel predictions in Drosophila melanogaster genomes

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dc.contributor.advisor Lau, Nelson Kanodia, Abhay 2016-03-14T15:12:25Z 2016-03-14T15:12:25Z 2016
dc.description.abstract Transposons are mobile genetic elements that make up a significant portion of metazoan genomes, such as ~12% of Drosophila melanogaster’s genome. Since active transposons can affect gene expression and genome structure, we need to track the frequency and the locations of where transposons will mobilize in the host genome. Recently, the Lau lab developed a software program called the Transposon Insertion and Deletion AnaLyzer (TIDAL) which can predict new Insertions and Depletions (InDels) in D. melanogaster genomes sequenced on the Illumina deep sequencing platform. The TIDAL program predicted several hundreds of transposon InDels in each genome of Drosophila cell lines and fly strains, but we did not know if these predictions are valid. To experimentally verify these predictions, we carried out a genomic PCR assay to test for the presence and absence of Transposable Element (TE) InDels predicted by TIDAL in a Drosophila cell line and fly strains genomes. By setting up new criteria to evaluate genomic PCR results, we could show that the majority of transposon InDels predicted by TIDAL could indeed be validated in cell lines and fly strains. Predictions made by TIDAL were compared to other programs like LnB (developed by Linheirro and Bergman), TEMP (developed the Zeng et al) and CnT (developed by Crindlad et al.). The validation rate was highest for predictions common to both TIDAL and LnB, and somewhat lower for InDels only predicted by TIDAL This lower rate of successful validations was also observed for TE insertions predicted by TEMP and CnT. Finally, we confirmed new TE InDels that have only recently emerged in the ISO1-BL fly strain that was used for making the Drosophila reference genome sequence and not found in ISO1-UC strain. In summary, our genomic PCR assay is capable of validating new TE InDels and supports the effectiveness of TIDAL.
dc.description.sponsorship Brandeis University, Graduate School of Arts and Sciences
dc.format.mimetype application/pdf
dc.language English
dc.language.iso eng
dc.publisher Brandeis University
dc.relation.ispartofseries Brandeis University Theses and Dissertations
dc.rights Copyright by Abhay Kanodia 2016
dc.subject D. melanogaster
dc.subject TIDAL
dc.subject Transposable Elements
dc.subject genomic PCR
dc.title Genomic PCR validation of InDel predictions in Drosophila melanogaster genomes
dc.type Thesis
dc.contributor.department Graduate Program in Molecular and Cell Biology MS Masters Molecular and Cell Biology Brandeis University, Graduate School of Arts and Sciences
dc.description.esploro yes

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