Abstract
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.
Highlights
Transposable elements (TEs) or transposons are found from widespread eukaryotic genomes [1]
During our screening of new transposable elements and re-classification of reported transposable elements, we found three distinct non-long terminal repeat (LTR) retrotransposon families that are associated with U2 small nuclear RNA (snRNA) genes
We found one nonLTR retrotransposon family from the jewel wasp Nasonia vitripennis (Utopia-1_NVit) is associated with fragment of U2 snRNA genes
Summary
Transposable elements (TEs) or transposons are found from widespread eukaryotic genomes [1]. Common target specificity in non-LTR retrotransposons encoding RLE allows us to speculate that during the early stages of their evolution, non-LTR retrotransposons were inserted in a target sequence-specific manner This speculation is reasonable since the probability of gene disruption by random integration depends on gene density, and target specificity is more advantageous in the smaller genomes of unicellular eukaryotes than in the larger ones of multicellular eukaryotes. We here report U2 small nuclear RNA (snRNA) gene-specific non-LTR retrotransposon families distributed among three eukaryotic supergroups: Amoebozoa, SAR and Opisthokonta. It indicates that these target-specific non-LTR retrotransposon families can be traced back to the period prior to the divergence of major eukaryotic supergroups
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