Three families of tRNA-derived repeated retroposons in the genomes of salmonid species have been isolated and characterized. These three families differ in sequence, but all are derived from a tRNALYS or from a tRNA species structurally related to tRNALyS. The salmon Sma I family is present in the genomes of two species of the genus Oncorhynchus but not in other species, including five other species of the same genus. The charr Fok I family is present only in four species and subspecies of the genus Salvelinus. The third family, the salmonid Hpa I family, appears to be present in all salmonid species but is not present in species that are not members of the Salmonidae. Thus, the genome of protoSalmonidae was originally shaped by amplification and dispersion of the salmonid Hpa I family and then reshaped by amplification of the Sma I and Fok I families in the more recently evolved species of salmon and charr, respectively. We speculate that amplification and dispersion of retroposons may have played a role in salmonid speciation.Gene duplication is believed to be of major importance in creating genetic diversity (1). The genes for immunoglobulins, histocompatibility complexes, and globins are examples of this gene duplication. This mechanism operates at the DNA level and probably has as old a history as DNA genomes themselves. Another mechanism for maintaining the fluidity of eukaryotic genomes is that recently characterized retroposition, in which information in nonviral cellular RNA can flow back into the genome via cDNA intermediates (2,3). Retroposition creates additional sequence combinations through dispersal of genetic information and can shape and reshape eukaryotic genomes in many different ways (3,4). The precise mechanism of retroposition is at present speculative. Recently, Weiner and Meizels (5) presented an interesting hypothesis concerning the mechanism of generation of duplex DNA at the beginning of the DNA world, proposing that duplex DNA genomes may have been derived from earlier DNA genomes that replicated like retroviruses through an RNA intermediate. This suggests that the mechanism of retroposition might be closely linked to that of replication of retroviruses (6).The highly repetitive sequences that are interspersed throughout eukaryotic genomes have been classified into two categories based on size: long interspersed repetitive elements (LINEs), which include Li sequences, and short interspersed repetitive elements (SINEs), such as the primate Alu and rodent type 1 or 2 Alu families (7). Previously, highly repetitive and transcribable sequences have been found in the genome of the chum salmon (Oncorhynchus keta) (8,9). Like all SINE families examined so far (10-14) other than Alu (15, 16), this Sma I family [formerly the salmon polymerase (Pol) III/SINE family] has been shown to be derived from a tRNA; moreover the Sma I family has several of the characteristic features of retroposons and appears to be the youngest SINE family characterized to date.The genus Oncorhynchus has many s...
The genomes of chum salmon and pink salmon contain a family of short interspersed repetitive elements (SINEs), designated the salmon SmaI family. It is restricted to these two species, a distribution that suggests that this SINE family might have been generated in their common ancestor. When insertions of the SmaI SINEs at 10 orthologous loci of these species were analyzed, however, it was found that there were no shared insertion sites between chum and pink salmon. Furthermore, at six loci where SmaI SINEs have been species-specifically inserted in chum salmon, insertions of SINEs were polymorphic among populations of chum salmon. By contrast, at four loci where SmaI SINEs had been species-specifically inserted in pink salmon, the SINEs were fixed among all populations of pink salmon. The interspecific and intraspecific variation of the SmaI SINEs cannot be explained by the assumption that the SmaI family was amplified in a common ancestor of these two species. To interpret these observations, we propose several possible models, including introgression and the horizontal transfer of SINEs from pink salmon to chum salmon during evolution.
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