2.9 Evolution of Repetitive Sequences

Summary. Three families oftRNA-derived SINE (short interspersed element) in the genomes of salmonid species were isolated and characterized. These three families, the salmon Sma I family, charr Fok I family and salmonid Hpa I family, differ in sequence, but are all derived from a lysine tRNA or a tRNA species struc­ turally related to lysine tRNA. These have been amplified at the specific stage of evolution ofsalmonid 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 I family, and then in the genome of some descendents the salmon Sma 1 or charr Fok I family was amplified and these genomes were again reshaped. In addition to several SINEs in salmonid species, it was found that the genome of tortoise contains repetitive sequences, designated tortoise Pol III/SINE, which is also derived from a lysine tRNA, showing that retroposons are prevalent in vertebrate species. To search for a similar kind of retroposon in invertebrate spe­ cies, in vitro transcription of total genomic DNA from various invertebrate species was performed. Sequences of repetitive families in squid and octopus were deter­ mined and it was found that they are tRNA-derived SINEs. The squid SINE is most similar to the lysine tRNA. The similarities of several SINEs including the human Alu to tRNAs were also reexamined. It was found that the human Alu can form a lysine tRNA-like structure, and Galago type II family, which was reported to be derived from a methionine initiator tRNA was also found to be the most similar to the lysine tRNA. Thus, lysine tRNA-like structures are widespread in genomes in the animal kingdom. The significance of these findings in relation to the evolution of salmonid species is discussed.