Investigating The Structural and Functional Roles Of Transcriptionally Active Rice Transposons

Authors

Eimaan Ahmad, Nova Southeastern UniversityFollow
Leelakrishna Angadala, Nova Southeastern UniversityFollow
Udhay Nallapati, Nova Southeastern UniversityFollow
Rushil Mehrotra, Nova Southeastern UniversityFollow
Braham Dhillon, University of Florida IFAS, Ft. Lauderdale Research & Education CenterFollow
Navi Gill Dhillon, Nova Southeastern UniversityFollow

Publication Date

2025

Keywords

transposable elements, sequencing technologies, PacBio, Nipponbare, rice

Abstract

Transposable elements (TEs) are notorious given their contributions to genome dynamics, evolution, gene structure, and regulation of gene expression. Famously once branded as ‘junk DNA’, TEs are now known to play significant roles in genome structure and function. Plethora of data generated from sequencing projects have advanced the study of transposons but their large size -often larger than read lengths of most sequencing platforms- has limited TE research due to limited coverages in sequenced datasets. Additionally, high copy number of TEs and high sequence similarity -often greater than 80%- between multiple copies of a TE family may lead to erroneous and misguided results. A limited number of sequencing technologies such as PacBio and Oxford Nanopore provide long reads capable of covering the entire transposon in a single read or generating high-quality assemblies of the region. In this study, we have used a PacBio RNAseq dataset of Oryza sativa var. Nipponbare and have functionally characterized the transcriptionally active full-length transposons in the rice genome. We have identified Genes Associated with these active Transposable Elements (GATEs) and found correlations of gene distribution and expression with TE coverages and TE expression levels. We are currently investigating if there is a preference or predisposition for TE insertions in housekeeping genes versus inducible genes and/or transcription factors. This will advance our understanding of how active TEs play functional roles in the genomes.

This Research has been presented

NSU- Undergraduate Student Research Symposium- Davie campus April 2025

Recommended Citation

Ahmad, Eimaan; Angadala, Leelakrishna; Nallapati, Udhay; Mehrotra, Rushil; Dhillon, Braham; and Gill Dhillon, Navi, "Investigating The Structural and Functional Roles Of Transcriptionally Active Rice Transposons" (2025). Bioinformatics. 13.
https://nsuworks.nova.edu/bioinformatics/13