CUR - The Council on Undergraduate Research

The Effects of Irradiation on Transposable Elements in Maize and Arabidopsis Genomes

Megan Davis, Raegan Hoefler, and Dr. Thomas Peterson, Department of Genetics, Development, and Cell Biology, Iowa State University, 2437 Pammel Drive, Ames IA 50011

Transposable elements (TEs) are DNA sequences that can change their position within the genome. While many TEs have negligible effects, others may interrupt genes or induce mutations. In the Maize and Arabidopsis genomes, most TEs are inactive, but it’s been suggested that environmental stressors may cause an increase in transposition events. Understanding the relationship between environmental stressors and TEs is important as we explore growing crops and sending humans to planets, like Mars, that have increased levels of irradiation in comparison to Earth. Here, we used X-ray radiation on both maize (W22) and Arabidopsis (TAIR10) and then assembled a bioinformatic pipeline to test the hypothesis that this stress will cause an increase in transposition events. Arabidopsis was exposed to 80 Gy of radiation while the Maize was exposed to 10 Gy of radiation. Each plant was grown and self-crossed for three generations before sample collection was performed in the third generation in order to ensure the fixation of activated transposable elements. Oxford Nanopore long-read sequencing was performed for both species and then reads were aligned to their respective reference genome using minimap2. SVIM, a bioinformatics tool designed to detect structural variants in long-read sequences, was used to find instances of novel insertions in the genomes. The novel insertions were then compared to the reference genome using the BLAST software, and the BLAST hits showed where the novel insertions aligned with the reference genome. The BLAST hits were then compared to the annotated transposons via bedtools intersect software and custom R code. Instances where the start and endpoints of the BLAST hits are close to the start and endpoints of the annotated transposons will be identified in order to locate active transposons. The results will indicate whether or not stress caused by irradiation will lead to an increase in transposon activity.

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