Dfam and Repbase Unite to Create a Fully Open Resource for Transposable Element Research

For more than three decades, researchers studying genomes have relied on foundational resources such as Repbase and, more recently, Dfam, to identify and classify transposable elements — the mobile DNA sequences that shape genome structure, evolution, and function. Now, Dfam and Repbase are coming together under a single, fully open framework.

A new paper published in Mobile DNA announces the integration of two of the most widely used resources for transposable element annotation. As part of the effort, the full Repbase collection will be released under a public-domain license, making decades of expertly curated transposable element data freely available to researchers worldwide.

The collaboration brings together the complementary strengths of the two resources. Founded in 1990 by the late Jerzy Jurka at the Genetic Information Research Institute (GIRI), Repbase became the gold standard for expertly curated transposable element consensus sequences. Dfam, launched in 2012 and led by researchers at ISB and the University of Arizona, has grown into one of the field’s leading open resources for large-scale genome annotation.

Together, the unified effort aims to provide researchers with a single, comprehensive resource that combines Repbase’s deep curation expertise with Dfam’s open infrastructure and broad taxonomic coverage.

“For years, researchers have depended on both resources,” said Robert Hubley, co-PI of the Dfam project at ISB. “By combining Repbase’s decades of expert curation with Dfam’s rich data representation, scalable infrastructure, and expanding analytical capabilities, researchers will gain access to a unified open platform that preserves the strengths of both projects.”

The agreement also marks a significant step forward for open science. Repbase has long been regarded as one of the field’s most important resources, but access to its data has historically been restricted by licensing requirements. Under the new arrangement, the complete collection will become openly available, allowing researchers around the world to use, share, and build upon the resource without restriction.

“Neither project could fully achieve this vision on its own,” said Dr. Travis Wheeler, professor at the University of Arizona and co-leader of the Dfam project. “This collaboration creates an opportunity to establish a unified foundation for transposable element research — one that combines the best features of both resources and can continue to grow alongside the needs of the genomics community.”

The integration effort will occur over multiple releases. Initial steps include making Repbase data openly available in its current form and developing methods to incorporate those curated records into the Dfam framework. Researchers will also work to reconcile overlapping entries, migrate specialized curation tools, and create new approaches for managing the rapidly growing volume of transposable element data generated by modern sequencing projects.

The collaboration is further strengthened by the participation of key members of the Repbase curation team, who will continue their work as part of the Dfam effort. Their expertise will help guide the integration of the two resources and support future advances in transposable element classification and annotation.

Researchers say the result will be a single, coherent resource capable of supporting projects ranging from the annotation of individual genomes to large-scale comparative studies spanning hundreds or thousands of species. The unified resource is expected to support applications ranging from evolutionary research and genome annotation to biomedical and agricultural research.

“This is a pivotal moment for open science in our field,” Hubley said. “Decades of knowledge and curation will now be freely available to researchers everywhere, helping accelerate discovery and enabling new generations of genomic research.”