Diversity and genome engineering applications of R2 non-LTR retrotransposons

The R2 retrotransposon family has been a leading model system for studies of site-specific non-long-terminal-repeat retrotransposon mobility. More recently, avian R2 systems have been harnessed to implement stable sequence supplementation of the human genome. Investigations of R2 retrotransposons range from detailed biochemical studies of purified components to elucidation of the cellular processes that support new retrotransposon insertions. In addition, molecular and genetic studies have examined the persistence and diversification of R2 retrotransposons across animals. In publications starting from early 2024, an R2-encoded protein has been used in native form, or after modification, to insert transgene sequences of choice into heterologous genomes lacking an endogenous R2. Many of these genome engineering studies were launched using a historically accumulated reporting of R2 sequences informative for understanding retrotransposon evolution but not intended as a catalogue of active R2 retrotransposons. Other groups approached R2 sequence identification by using or building consensus retrotransposon sequences from mostly short-read genome sequencing or genome assemblies. Here, we describe R2 sequence discovery, phylogeny, and annotation, and we consider their influence on R2 protein applications including gene addition to the human genome.