The salmon SmaI family of short interspersed repetitive elements (SINEs): Interspecific and intraspecific variation of the insertion of SINEs in the genomes of chum and pink salmon

Genetics

Volumn 146, Issue 1, 1997, Pages 369-380

  Takasaki, Nobuyoshi ^a   Yamaki, Toshifumi ^a   Hamada, Mitsuhiro ^a   Park, Linda ^b   Okada, Norihiro ^a  

^a TOKYO INSTITUTE OF TECHNOLOGY   (Japan)

^b NORTHWEST FISHERIES SCIENCE CENTER   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; GENE INSERTION; GENE LOCUS; GENE TRANSFER; GENETIC VARIABILITY; NONHUMAN; PRIORITY JOURNAL; SALMON; SHORT INTERSPERSED REPEAT; SPECIES DIFFERENCE;

EID: 0030902263     PISSN: 00166731     EISSN: None     Source Type: Journal    
DOI: None     Document Type: Article

References (50)

1. ARNOLD, M. L., 1992 Natural hybridization as an evolutionary process. Annu. Rev. Ecol. Syst. 23: 237-261.
2. AUBERT, J., and M. SOLIGNAC, 1990 Experimental evidence for mitochondrial DNA introgression between Drosophila species. Evolution. 44: 1272-1282.
3. BATZER, M. A., and P. L. DEININGER, 1991 A human-specific subfamily of Alu sequences. Genomics 9: 481-487.
4. BATZER, M. A., V. A. GUDI, J. C. MENA, D. W. FOLTZ, R. J. HERREA et al., 1991 Amplification dynamics of human-specific (HS) alu family members. Nucleic Acids Res. 19: 3619-3623
5. BATZER, M. A., M. STONEKING, M. ALEGRIA-HARTMAN, H. BAZEN, D. H. KASS et al., 1994 African origin of human-specific polymorphic Alu insertions. Proc. Natl. Acad. Sci. USA 91: 12288-12292.
6. BLIN, N. and D. W. STAFFORD, 1976 A general method for isolation of high molecular weight DNA from eukaryotes. Nucleic Acids Res. 3: 2303-2308.
7. DEININGER, P. L. and M. A. BATZER, 1993 Evolution of retroposons, pp. 157-196 in Evolutionary Biology, Vol. 27, edited by M. K. HECHT et al. Plenum Press, New York.
8. DERAGON, J.-M., B. S. LANDRY, T. PELISSIER, S. TUTOIS, S. TOURMENTE et al., 1994 An analysis of retroposition in plants based on a family of SINEs from Brassica napus. J. Mol. Evol. 39: 378-386
9. DOWLING, T. E., and B. D. DEMARAIS, 1993 Evolutionaiy significance of introgressive hybridization in cyprinid fishes. Nature 362: 444-446.
10. FERGUSON, A., and C. C. FLEMING, 1983 Evolutionary and taxonomic significance of protein variation in the brown trout (Salmo trurra L.) and other salmonid fishes, pp. 85-99 in Protein Polymorphism: Adaptive and Taxonomic Significance, edited by G. S. OXFORD, and D. ROLLINSON. Academic Press, London.
11. GHARRETT, A. J., C. SMOOT and A. J. MCGREGOR, 1988 Genetic relationships of even-yesr northwestern Alaskan pink salmon. Trans. Am. Fish. Soc. 117: 536-545.
12. GINATULINA, L. K., S. V. SHEDKO, I. L. MIROSHNICHENKO and A. A. GINATULIN, 1988 Sequence divergence in mitochondrial DNA from the Pacific salmons. Zhurnal Evolyusionnoy Biokhimii Fiziologii. J. Mol. Biol. Physiol. 24: 477-483 (in Russian).
13. GROOT, C., and L. MARGOLIS (Editors), 1991 Pacific Salmon Life Histories, UBC Press, Vancouver, British Columbia, Canada.
14. HAMADA, M., Y. KIDO, M. HIMBERG, J. D. REIST, Y. CAO et al., 1997 A newly isolated family of short interspersed repetitive elements (SINEs) in coregonid fishes (whitefish) with sequences that are almost identical to those of the SmaI family of repeats: possible evidence for the horizontal transfer of SINEs. Genetics 146: 355-367.
15. HARRISON, R. G., 1990 Hybrid zones: windows on evolutionary process. Oxf. Surv. Evol. Biol. 7: 69-127.
16. HOAR, W. S., 1958 The evolution of migratory behaviour among juvenile salmon of the genus Oncorhynchus. J. Fish. Res. Board Can. 15: 391-428.
17. JAGADEESWAREN, P., B. G. FORGET and S. M. WEISSMAN, 1981 Short interspersed repetitive DNA elements in eucaryotes: transposable DNA elements generated by reverse transcription of RNA pol III transcripts? Cell 26: 141-142.
18. KIDO, Y., M. AONO, T. YAMAKI, K. MATSUMOTO, S. MURATA et al., 1991 Shaping and reshaping of salmonid genomes by amplification of tRNA-derived retroposons during evolution. Proc. Natl. Acad. Sci. USA 88: 2326-2330.
19. KIDO, Y., M. HIMBERG, N. TAKASAKI and N. OKADA, 1994 Amplification of distinct subfamilies of short interspersed elements during evolution of the Salmonidae. J. Mol. Biol. 241: 633-644.
20. KIDO, Y., M. SAITO, S. MURATA and N. OKADA, 1995 Evolution of the active sequences of the HpaI short interspersed elements. J. Mol. Evol. 41: 986-995.
21. KOISHI, R., and N. OKADA, 1991 Distribution of the salmonid Hpa I family in salmonid species demonstrated by in vitro runoff transcription assay of total genomic DNA: a procedure to estimate repetitive frequency and sequence divergence of a certain repetitive family with a few known sequences. J. Mol. Evol. 32: 43-52.
22. MATSUMOTO, K., K. MURAKAMI and N. OKADA, 1986 Gene for lysine tRNA, may be a progenitor of the highly repetitive and transcribable sequences present in the salmon genome. Proc. Natl. Acad. Sci. USA 83: 3156-3160.
23. MOCHIZUKI, K., M. UMEDA, H. OHTSUBO and E. OHTSUBO, 1992 Characterization of a plant SINE, p-SINE1, in rice genome. Jpn. J. Genet. 67: 155-166.
24. MURATA, S., N. TAKASAKI, M. SAITOH and N. OKADA, 1993 Determination of the phylogenetic relationships among Pacific salmonids by using short interspersed elements (SINEs) as temporal landmarks of evolution. Proc. Natl. Acad. Sci. USA 90: 6995-6999.
25. MURATA, S., N. TAKASAKI, M. SAITOH, H. TACHIDA and N. OKADA, 1996 Details of retropositional genome dynamics that provide a rationale for a genetic division: the distinct branching of all the pacific salmon and trout (Oncorhynchus) from the Atlantic salmon and trout (Salmo). Genetics 142: 915-926.
26. OHSHIMA, K., R. KOISHI, M. MATSUO and N. OKADA, 1993 Several short interspersed repetitive element (SINEs) in distant species may have originated from a common ancestral retrovirus: characterization of a squid SINE and a possible mechanism for generation of tRNA-derived retroposons. Proc. Natl. Acad. Sci. USA 90: 6260-6264.
27. OKADA, N., 1991a SINEs: Short interspersed repeated elements of the eukaryotic genome. Trends Ecol. Evol. 6: 358-361.
28. OKADA, N., 1991b SINEs. Curr. Opin. Genet. Dev. 1: 498-504.
29. OKADA, N., and K. OHSHIMA, 1995 Evolution of tRNA-derived SINEs, pp. 61-79 in The Impact of Short Interspersed Elements (SINEs) on the Host Genome, edited by R. MARAIA. R. G. Landes Company, Austin, TX.
30. PERNA, N. T., M. A. BATZER, P. L. DEININGER and M. STONEKING, 1992 Alu insertion polymorphism: a new type of marker for human population studies. Hum. Biol. 64: 641-648.
31. PHILLIPS, R. B., K. A. PLEYTE and M. R. BROWN, 1992 Salmonid phylogeny inferred from ribosomal DNA restriction maps. Can. J. Fish. Aquat. Sci. 49: 2345-2353.
32. RIESEBERG, L. H., and D. E. SOLTIS, 1991 Phylogenetic consequences of cytoplasmic gene flow in plants. Evol. Trends Plants 5: 65-84.
33. ROGERS, J. H., 1985 The origin and evolution of retroposons. Int. Rev. Cytol. 93: 187-279.
34. SCHMID, C. and R. MARAIA, 1992 Transcriptional regulation and transpositional selection of active SINE sequences. Curr. Opin. Genet. Dev. 2: 874-882.
35. SHEDLOCK, A. M., J. D. PARKER, D. A. CRISPIN, T. W. PIETSCH and G. C. BURMER, 1992 Evolution of the salmonid mitochondrial control region. Mol. Phylogenet. Evol. 1: 179-192.
36. SINGER, M. F., 1982 SINEs and LINEs: Highly repeated short and long interspersed sequences in mammalian genomes. Cell 28: 433-434.
37. SMIT, A. F., 1996 The origin of interspersed repeats in the human genome. Curr. Opin. Genet. Dev. 6: 743-748.
38. SMITH, G. R., 1992 Introgression in fishes: significance for paleontology, cladistics, and evolutionary rates. Syst. Biol. 41: 41-57.
39. SMITH, G. R., and R. F. STEARLEY, 1989 The classification and scientific names of rainbow and cutthroat trouts. Fisheries 14: 4-10.
40. STEARLEY, R. F., and G. R. SMITH, 1993 Phylogeny of the Pacific trouts and salmons (Oncorhynchus) and genera of the family Salmonidae. Trans. Am. Fish. Soc. 122: 1-33.
41. STEIT, B., T. STÄDLER, K. SCHWENK, A. ENDER, K. KUHN et al., 1994 Natural hybridization in freshwater animals; ecological implications and molecular approaches. Naturwissenschaften 81: 65-73.
42. TAKASAKI, N., S. MURATA, M. SAITOH, T. KOBAYASHI, L. PARK et al., 1994 Species-specific amplification of tRNA-derived short interspersed repetitive elements (SINEs) by retroposition: a process of parasitization of entire genomes during the evolution of salmonids. Proc. Natl. Acad. Sci. USA 91: 10153-10157.
43. TAKASAKI, N., L. PARK, M. KAERIYAMA, A. J. GHARRETT and N. OKADA, 1996 Characterization of species-specifically amplified SINEs in three salmonid species, chum salmon, pink salmon, and kokanee: the local environment of the genome might be important for the generation of a dominant source gene at a newly retroposed locus. J. Mol. Evol. 42: 103-116.
44. TAYLOR, D. J., and P. D. N. HEBERT, 1992 Daphnia galeata mendotae as a cryptic species complex with interspecific hybrids. Limnol. Oceanogr. 37: 651-657.
45. THOMAS, W. K., R. E. WITHLER and A. T. BECKENBACH, 1986 Mitochondrial DNA analysis of Pacific salmonid evolution. Can. J. Zool. 64: 1058-1064.
46. ULLU, E., and C. TSCHUDI, 1984 Alu sequences are processed 7SL RNA genes. Nature 312: 171-172.
47. UTTER, F. M., F. W. ALLENDORF and H. O. HODGINS, 1973 Genetic variability and relationships in Pacific salmon and related trout based on protein variations. Syst. Zool. 22: 257-270.
48. WEINER, A. M., 1980 An abundant cytoplasmic 7S RNA is complementary to the dominant interspersed middle repetitive DNA sequence family in the human genome. Cell 22: 209-218.
49. WENDEL, J. F., A. SCHNABEL and T. SEELANAN. 1995 An unusual ribosomal DNA sequence from Gossypium gossypioides reveals ancient, cryptic, intergenomic introgression. Mol. Phylogenet. Evol. 4: 298-313.
50. YOSHIOKA, Y., S. MATSUMOTO, S. KOJIMA, K. OHSHIMA, N. OKADA et al., 1993 Molecular characterization of a short interspersed repetitive element from tobacco that exhibits sequence homology to specific tRNAs. Proc. Natl. Acad. Sci. USA 90: 6562-6566.