Evolution of Sequencing Technologies and Implications for Transposon Research

This study explores the complex field of transposable elements (TEs) and how Next Generation Sequencing (NGS) technologies are used to identify them, including their limitations. Transposons, also known as transposable elements, are dynamic DNA segments that have the ability to shift locations within a genome, impacting gene regulation, evolutionary processes, and genomic stability. TEs play vital roles in genetic research. They provide pathways for precise genetic alterations and mutagenesis, which facilitate the investigation of gene function and disease mechanisms in many organisms. Rapid DNA and RNA sequencing capabilities provided by NGS technologies have transformed genetic research. Improvements in effective DNA sequencing techniques have greatly improved our knowledge of diseases and potential treatments by generating a plethora of sequence information at a relatively low cost. This has significantly improved the identification and analysis of TEs, even from short-read NGS technologies, resulting in better understanding of the functions and implications of TEs in the genome. However, certain limitations exist in TE research. TEs belonging to a given family share high sequence similarity to each other. This along with the fact that TEs are present as multiple copies in the genome, makes their identification and annotation challenging. With advances in NGS long-read technologies, we can better address these issues by effectively standardizing processes for TE identification and annotation. In this study, we compare the advancements in NGS methods and their implications on TE research with an objective to facilitate efficient identification and characterization of TES to fully understand their applications in genetic research.