Active and unusually expanded PIF/Harbinger transposable elements in the Caenorhabditis inopinata genome

Abstract Understanding how transposable elements (TEs) transition from rapid amplification to functional decay is fundamental to unraveling the mechanisms of genome evolution and structural variation. How TE families evolve following expansion, specifically why distinct descendant lineages retain or lose mobilisation competence, remains poorly understood. The PIF/Harbinger superfamily, whose canonical elements encode two distinct proteins required for mobilisation—a DDE transposase and a MADF DNA-binding protein—provides a compelling model to address this question. In Caenorhabditis inopinata, the closest known relative of C. elegans, we identified a spontaneous dumpy mutant caused by insertion of a PIF/Harbinger element into the Cin-dpy-11 coding region. The inserted element, designated Harbinger-1M_cIno and belonging to the C. elegans Turmoil2 lineage, retains a MADF domain but lacks a recognisable DDE transposase open reading frame. Genome-wide curation recovered 258 related copies, revealing a strongly asymmetric family structure: noncoding and MADF-bearing derivatives expanded, whereas only a single locus retained an intact DDE gene. This demonstrates a novel functional partitioning where catalytic (DDE) and DNA-binding (MADF) roles are physically separated across distinct elements and supplied in trans. A second family, Harbinger-2M_cIno (1,376 copies), lacks a DDE source entirely and exhibits greater sequence divergence and terminal degradation. Together, these findings reveal that PIF/Harbinger lineages in C. inopinata differ in their timing of expansion and mobilisation competence, illustrating how bipartite TEs maintain activity through functional division while limiting host toxicity.