Recombinant Repeats in Mammalian Genomes: Evolutionary Junk or Experimental Products to Create Novel Transposable Elements?

Transposable elements are major components of eukaryotic genomes. They were first discovered by Barbara McClintock in 1948, in maize. Current studies have shown that transposable elements not only drive genome evolution and are correlated with speciation, they also create unique structural variation in individuals.  However, the potential of transposable elements to create novel repetitive elements (recombinant repeats) in eukaryotic genomes is still largely unclear and unexplored. Here we report on a detailed analysis of recombinant repeats in several mammalian genomes. Our computational approach has discovered over 30,000 recombinant repeats in different mammalian genomes that can be divided into different families based on their structures and sequences. Our data suggest that LINE (Long interspersed nuclear element) and SINE (Short interspersed nuclear element) retrotransposons are the major transposable elements that create new recombinant repeats. Some of these recombinant repeats contain ancestral transposable elements, indicating that these processes have been occurring since before the mammalian radiation. Our data also show that recombinant repeats were primarily generated through active insertion events and not through a reverse transcriptase template switching mechanism. Some recombinant repeats contain recent target site duplication (TSDs), suggesting that they are retrotranspositionally active. Our results provide strong support for the notion that recombinant repeats are experimental evolutionary by-products of the processes that create novel transposable elements in mammalian genomes, and that they can serve as potential genetic markers to resolve phylogenetic trees.