Recurrent Modular Assembly Drives Independent Origins of Group II Introns Encoding LAGLIDADG Homing Endonucleases

Abstract Group II introns are catalytic RNAs that typically mobilize with intron-encoded reverse transcriptase/maturase (RT/M) proteins, yet a small subset encodes LAGLIDADG homing endonucleases (LHEs). The evolutionary mechanisms underlying this atypical RNA–protein association remain poorly understood. Here, we analyze 753 LHE-encoding group II introns (group II-LHE introns) from green algae, fungi, and bacteria to investigate their origins and structural diversification. Our comparative analyses reveal that these introns are distributed across four deeply divergent RNA backbone subclasses (IIA1, IIB1, IIB2, IIC) and form 13 lineage-specific intron families. Secondary-structure reconstruction reveals a conserved catalytic core together with extensive family-specific remodeling, including variable LHE insertion sites, recurrent loss of branch-point adenosine, and differential retention of exon-recognition elements. Phylogenetic incongruence between the RNA backbone and LHE phylogenies supports multiple independent acquisitions rather than descent from a single ancestral composite element. These results demonstrate that LHE modules have been repeatedly recruited onto distinct group II intron scaffolds, highlighting recurrent modular assembly as a key mechanism in the evolution of RNA-protein mobile elements. Our study provides a unified framework for understanding the origin, diversification, and modular evolution of LHE-encoding group II introns.