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Characterization of species-specifically amplified SINEs in three salmonid species—Chum salmon, pink salmon, and kokanee: The local environment of the genome may be important for the generation of a dominant source gene at a newly retroposed locus

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Abstract

Short interspersed repetitive elements (SINEs), known as theHpaI family, are present in the genomes of all salmonid species (Kido et al.,Proc. Natl. Acad. Sci. USA 1991, 88: 2326–2330). Recently, we showed that the retropositional efficiency of the SINE family in the lineage of chum salmon is extraordinarily high in comparison with that in other salmonid lineages (Takasaki et al.,Proc. Natl. Acad. Sci. USA 1994, 91: 10153–10157). To investigate the reason for this high efficiency, we searched for members of theHpaI SINE family that have been amplified species-specifically in pink salmon. Since the efficiency of the species-specific amplification in pink salmon is not high and since other members of the same subfamily of SINEs were also amplified species-specifically in pink salmon, the actual sequence of this subfamily might not be the cause of the high retropositional efficiency of SINEs in chum salmon. Rather, it appears that a highly dominant source gene for the subfamily may have been newly created by retroposition, and some aspect of the local environment around the site of retroposition may have been responsible for the creation of this dominant source gene in chum salmon. Furthermore, a total of 11 sequences ofHpaI SINEs that have been amplified species-specifically in three salmon lineages was compiled and characterized. Judging from the distribution of members of the same-sequence subfamily of SINEs in different lineages and from the distribution of the different-sequence subfamilies in the same lineage, we have concluded that multiple dispersed loci are responsible for the amplification of SINEs. We also discuss the additional possibility of horizontal transmission of SINEs between species. The availability of the sets of primers used for the detection of the species-specific amplifications of the SINEs provides a convenient and reliable method for identification of these salmonid species.

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Authors and Affiliations

  1. Faculty of Bioscience and Biotechnology, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, 226, Yokohama, Japan

    Nobuyoshi Takasaki & Norihiro Okada

  2. Northwest Fisheries Science Center, Coastal Zone and Estuarine Studies Division, 2725 Montlake Boulevard East, 98112-2097, Seattle, WA, USA

    Linda Park

  3. Hokkaido Salmon Hatchery, Fisheries Agency of Japan, 2-2 Nakanoshima, Toyohira-ku, 062, Sapporo, Japan

    Masahide Kaeriyama

  4. Juneau Center, School of Fisheries and Ocean Sciences, University of Alaska Fairbanks, 11120 Glacier Highway, 99801, Juneau, AK, USA

    Anthony J. Gharrett

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  1. Nobuyoshi Takasaki
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  2. Linda Park
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  4. Anthony J. Gharrett
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  5. Norihiro Okada
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Takasaki, N., Park, L., Kaeriyama, M. et al. Characterization of species-specifically amplified SINEs in three salmonid species—Chum salmon, pink salmon, and kokanee: The local environment of the genome may be important for the generation of a dominant source gene at a newly retroposed locus. J Mol Evol 42, 103–116 (1996). https://doi.org/10.1007/BF02198835

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