SINE retrotransposition during the evolution of the pecoran ruminants

SINE retrotransposition events have proven their value as phylogenetic mark ers in several eukaryotic taxa at different taxonomic levels. The genomes o f ruminants contain three related SINE elements, Bov-tA. Bov-A2, and Bov-B. To estimate the time points of retrotransposition of individual copies of these SINEs, we designed PCR primers on database sequences containing SINE insertions in cattle, sheep, or goat genomes and tested for the presence of these copies in the genomes of other ruminants. It was checked by sequenci ng whether length variation of the PCR products reflected a SINE retrotrans position. One Bov-B and nine Bov-tA insertions were shared by cattle, sheep , goat, and giraffe. indicating an early retrotransposition event before th e radiation of the Pecora, while three other Bov-tA and two Bov-B elements were apparently inserted later. The ruminant alpha -lactalbumine gene conta ins a hotspot of early and more recent Bov-tA insertions, a Bov-tA replacem ent as well as a recent Bov-B insertion. Three Bov-A2 insertions were found to be shared only by the Bovidae, the Bovini, and the Bos and Bison specie s, respectively, indicating that most Bov-A2 insertions are relatively rece nt. The time elapsed since the retrotransposition was also reflected in the degeneration of the direct repeats that flank SINE inserts. We suggest tha t retrotransposition of SINEs may serve as phylogenetic markers in the rumi nant families, subfamilies, and even tribes. In addition., sequencing of SI NE insertions revealed several other unique deletions/insertions that also may be informative for phylogenetic reconstructions of ruminants.