Evolution of Repetitive Sequences

Three families of tRNA-derived SINE (short interspersed element) in the genomes of salmonid species were isolated and characterized. These three families, the salmon Sma 1 family, charr Fok 1 family and salmonid Hpa 1 family, differ in sequence, but are all derived from a lysine tRNA or a tRNA species structurally related to lysine tRNA. These have been amplified at the specific stage of evolution of salmonid species. The average sequence divergence of the salmon Sma 1 family, charr Fok 1 family and salmonid Hpa 1 family are roughly 0.7%, 0.9%, and 3.1% respectively, showing that the Sma 1 family amplified the most recently and that the Hpa 1 family is the oldest. There is a parallel between these values and distribution at a different position in the phylogenic tree of these families in the salmonid species. Thus, the genome in the proto-Salmonidae was first shaped by amplification and dispersion of the salmonid Hpa 1 family, and then in the genome of some descendents the salmon Sma 1 or charr Fok 1 family was amplified and these genomes were again reshaped.