Irvine, Calif., March 24, 2025 — Why do genetic recombination rates — the process that reshuffles DNA during reproduction — vary so widely between individuals and species? A new study from UC Irvine’s Charlie Dunlop School of Biological Sciences, published in Proceedings of the National Academy of Sciences, has uncovered a surprising answer: mobile genetic elements known as transposable elements (TEs) actively suppress recombination, fundamentally shaping genetic variation.
Led by Assistant Professor Grace Lee, the research challenges long-held assumptions about genome evolution. Scientists have traditionally believed that TEs accumulate in low-recombination regions because these areas offer fewer opportunities for natural selection to remove them. However, this study flips that idea on its head, showing that TEs may actually cause low recombination rates by altering the surrounding genetic environment.
“We employed three complementary approaches to demonstrate that transposable elements reduce local recombination rates,” said Lee. “A particularly powerful aspect of our study is our comparison between nearly identical homologous sequences that differ only in the presence or absence of TEs, effectively eliminating other confounding local effects.”
To track recombination events with high precision, the team developed a novel sequencing technique using PacBio long-read sequencing. Their results showed that RNA-based TEs, as well as those enriched with specific epigenetic marks, significantly reduce the frequency of recombination. This suppression influences how genes are inherited, potentially affecting evolutionary trajectories and species diversity.
Validating this new approach was no small feat. “One of our most significant challenges was validating the PacBio long-read sequencing approach for our research question,” Dr. Huang, the first author of the study, explained. “To establish its feasibility, we generated benchmark data and compared it against our sequencing results to identify potential confounding effects. We then confirmed these findings through targeted simulations, which also helped us determine the optimal conditions for implementing this approach effectively.”
The discovery that TEs actively shape recombination landscapes has major implications beyond evolutionary biology. Understanding how they influence genome structure could shed light on the mechanisms behind genetic disorders, help refine breeding strategies in agriculture and offer new perspectives on genome stability.
“Since recombination rate is a key determinant of genome evolution, the critical question now is how these newly discovered impacts of TEs shape genome variation and evolutionary trajectories through their suppressive effects on recombination patterns,” said Lee. “Future research should focus on quantifying the evolutionary significance of TE-mediated recombination suppression across diverse taxa and genomic contexts.”
The study represents a major step forward in understanding how dynamic genetic elements contribute to evolution. As researchers continue to explore the implications of this discovery, it may lead to new insights into genetic adaptation, conservation biology and medical genetics.
About the University of California, Irvine Charlie Dunlop School of Biological Sciences:
Recognized for its pioneering research and academic excellence, the Charlie Dunlop School of Biological Sciences plays a crucial role in the university’s status among the nation’s top 10 public universities, as ranked by U.S. News & World Report. It offers a broad spectrum of degree programs in the biological sciences, fostering innovation and preparing students for leadership in research, education, medicine and industry. Nestled in a globally acclaimed and economically vibrant community, the school contributes to the university’s impact as Orange County’s largest employer and a significant economic contributor. Through its commitment to exploring life’s complexities, the Dunlop School embodies the UCI legacy of innovation and societal impact. For more on the Charlie Dunlop School of Biological Sciences, visit https://www.bio.uci.edu/.