Publication Date
2026
Keywords
transposable elements, sequencing platforms
Abstract
Transposable elements (TEs) are mobile DNA sequences that make up a substantial portion of eukaryotic genomes and play key roles in gene regulation, genome evolution, and structural variation. Although short-read next-generation sequencing (NGS) platforms enabled large-scale detection of repetitive elements, their limited read lengths have long hindered accurate assembly and annotation of TEs, many of which consist of highly similar, multi-copy sequences exceeding the size of typical reads. Recent advances in long-read sequencing technologies such as Pacific Biosciences (PacBio) HiFi and Oxford Nanopore Technologies (ONT) have greatly improved TE research by generating long contiguous reads that span complete TE insertions, resolve repetitive regions, and capture epigenetic information such as methylation. These capabilities enable more precise characterization of both Class I retrotransposons and Class II DNA transposons and provide deeper insight into TE-driven regulatory and evolutionary processes. Comparative evaluations indicate that PacBio HiFi currently offers the most accurate TE reconstruction, with ONT providing complementary strengths for specific applications. This review summarizes major developments in sequencing technology and their implications for TE discovery, assembly, and functional analysis. We also highlight gaps between TE sizes and sequencing read lengths, the need for TE-aware computational tools for improving TE annotation and understanding genome dynamics.
Recommended Citation
Ahmad, Eimaan; Some, Mahalaxmi; and Gill Dhillon, Navi, "Advances in Sequencing Technologies and Their Impact on Transposable Element Discovery and Functional Analysis" (2026). Bioinformatics. 8.
https://nsuworks.nova.edu/bioinformatics/8
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