Multiple lineages of the non-LTR retrotransposon Rex1 with varying successin invading fish genomes

Rex1, together with the related Babar elements, represents a new family of non-long-terminal-repeat (non-LTR) retrotransposons from fish, which might be related to the CRI clade of LINE elements. Rex1/Babar retrotransposons e ncode a reverse transcriptase and an apurinic/apyrimidinic endonuclease, wh ich is very frequently removed by incomplete reverse transcription. Differe nt Rex1 elements show a conserved terminal 3' untranslated region followed by oligonucleotide tandem repeats of variable size and sequence. Phylogenet ic analysis revealed that Rex1 retrotransposons were frequently active duri ng fish evolution. They formed multiple ancient lineages, which underwent s everal independent and recent bursts of retrotransposition and invaded fish genomes with varying success (from <5 to 500 copies per haploid genome). A t least three of these ancient Rex1 lineages were detected within the genom e of poeciliids. One lineage is absent from some poeciliids but underwent s uccessive rounds of retrotransposition in others, thereby increasing its co py number from <10 to about 200. At least three ancient Rex1 lineages were also detected in the genome project fish Fugu rubripes. Rex1 distribution w ithin one of its major Lineages is discontinuous: Rex1 was found in all Aca nthopterygii (common ancestor in the main teleost lineage approximately 90 MYA) and in both European and Japanese eels (divergence from the main teleo st Lineage about 180 MYA) but not in trout, pike, carp, and zebrafish (dive rgence 100-120 MYA). This might either result from frequent loss or rapid d ivergence of Rex1 elements specifically in some fish lineages or represent one of the very rare examples of horizontal transfer of non-LTR retrotransp osons. This analysis highlights the dynamics and complexity of retrotranspo son evolution and the variability of the impact of retrotransposons on vert ebrate genomes.