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Most non-long terminal repeat (non-LTR) retrotransposons encoding a restriction-like endonuclease show target-specific integration into repetitive sequences such as ribosomal RNA genes and microsatellites. However, only a few target-specific lineages of non-LTR retrotransposons are distributed widely and no lineage is found across the eukaryotic kingdoms. Here we report the most widely distributed lineage of target sequence-specific non-LTR retrotransposons, designated  Utopia .  Utopia  is found in three supergroups of eukaryotes: Amoebozoa, SAR, and Opisthokonta.  Utopia  is inserted into a specific site of U2 small nuclear RNA genes with different strength of specificity for each family.  Utopia  families from oomycetes and wasps show strong target specificity while only a small number of  Utopia  copies from reptiles are flanked with U2 snRNA genes. Oomycete  Utopia  families contain an “archaeal” RNase H domain upstream of reverse transcriptase (RT), which likely originated from a plant RNase H gene. Analysis of  Utopia  from oomycetes indicates that multiple lineages of  Utopia  have been maintained inside of U2 genes with few copy numbers. Phylogenetic analysis of RT suggests the monophyly of  Utopia , and it likely dates back to the early evolution of eukaryotes.

Ancient Origin of the U2 Small Nuclear RNA Gene-Targeting Non-LTR Retrotransposons Utopia