Evolutionary relationships among rice species with AA genome based on SINE insertion analysis

Genes and Genetic Systems

Volumn 77, Issue 5, 2002, Pages 323-334

  Cheng, Chaoyang ^a   Tsuchimoto, Suguru ^a   Ohtsubo, Hisako ^a   Ohtsubo, Eiichi ^a  

^a UNIVERSITY OF TOKYO   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

AFRICA; ARTICLE; ASIA; GENE INSERTION; GENE LOCUS; GENETIC POLYMORPHISM; GENETIC VARIABILITY; GENOME; MARKER GENE; MOLECULAR EVOLUTION; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENETIC TREE; PLANT GENETICS; RETROPOSON; RICE; STRAIN DIFFERENCE; DIPLOIDY; GENETICS; MOLECULAR GENETICS; PHYLOGENY; SHORT INTERSPERSED REPEAT; TRANSPOSON;

ORYZA BARTHII; ORYZA GLABERRIMA; ORYZA LONGISTAMINATA; ORYZA MERIDIONALIS; ORYZA RUFIPOGON; ORYZA SATIVA; ZIZANIA;

BASE SEQUENCE; DIPLOIDY; DNA TRANSPOSABLE ELEMENTS; EVOLUTION, MOLECULAR; MOLECULAR SEQUENCE DATA; ORYZA SATIVA; PHYLOGENY; SHORT INTERSPERSED NUCLEOTIDE ELEMENTS;

EID: 0036814150     PISSN: 13417568     EISSN: None     Source Type: Journal    
DOI: 10.1266/ggs.77.323     Document Type: Article

References (45)

1. Aggarwal, R. K., Brar, D. S., and Khush, G. S. (1997) Two new genomes in the Oryza complex identified on the basis of molecular divergence analysis using total genomic DNA hybridization. Mol. Gen. Genet. 254, 1-12.
2. Aggarwal, R. K., Brar, D. S., Nandi, S., Huang, N., and Khush, G. S. (1999) Phylogenetic relationships among Oryza species revealed by AFLP markers. Theor. Appl. Genet. 98, 1320-1328.
3. Altschul, S. F., Gish, W., Miller, W., Myers, E. W., and Lipman, D. J. (1990) Basic local alignment search tool. J. Mol. Biol. 215, 403-410.
4. Bailey, A. D., and Shen, C. K. J. (1993) Sequential insertion of Alu family repeats into specific genomic sites of higher primates. Proc. Natl. Acad. Sci. USA 90, 7205-7209.
5. Bailey, A. D., and Shen, C. K. J. (1997) Molecular origin of the mosaic sequence arrangements of higher primate a-globin duplication units. Proc. Natl. Acad. Sci. USA 94, 5177-5182.
6. Batzer, M. A., Stoneking, M., Alegria-Hartman, M., Bazan, H., Kass, D. H., Shaikh, T. H., Novick, G. E., Ioannou, P. A., Scheer, W., D. Herrera, R. J., and Deininger, P. L. (1994) African origin of human-specific polymorphic Alu insertions. Proc. Natl. Acad. Sci. USA 91, 12288-12292.
7. Bautista, N. S., Solis, R., Kamijima, O., and Ishii, T. (2001) RAPD, RFLP and SSLP analysis of phylogenetic relationships between cultivated and wild species of rice. Genes Genet. Syst. 76, 71-79.
8. Brar, D. S., and Khush, G. S. (1997) Alien introgression in rice. Plant Mol. Biol. 35, 35-47.
9. Chang, T.-T. 1976. The origin, evolution, cultivation, dissemination and diversification of Asian and African rice. Euphytica 25, 425-441.
10. Cheng, C., Tsuchimoto, S., Ohtsubo, H., and Ohtsubo, E. (2000) Tnr8, a foldback transposable element from rice. Genes Genet. Syst. 75, 327-333.
11. Chu, Y. E., and Oka, H. I. (1970) The genetic basis of crossing barriers between Oryza perennis subsp. barthii and its related taxa. Evolution 24, 135-144.
12. Chu, Y. E., Morishima, H. and Oka, H. I. (1969a) Partial self-incompatibility in Oryza perennis subsp. barthii. Jpn. J. Genet. 44, 225-229.
13. Chu, Y. E., Morishima, H. and Oka, H. I. (1969b) Reproductive barrier distributed in cultivated rice species and their wild relatives. Jpn. J. Genet. 44, 207-223.
14. Ge, S., Sang, T., Lu, B.-R., and Hong, D.-Y. (1999) Phylogeny of rice genome with emphasis on origins of allotetraploid species. Proc. Natl. Acad. Sci. USA 96, 14400-14405.
15. Ghesquiere, A. (1986) Evolution of Oryza longistaminata. In: Rice Genetics, pp. 15-25. IRRI, Manila.
16. Hamada, M., Takasaki, N., Reist, J. D., Decicco, A. L., Goto, A., and Okada, N. (1998) Detection of the ongoing sorting of ancestrally polymorphic SINEs toward fixation or loss in populations of two species of charr during speciation. Genetics 150, 301-311.
17. Hamdi, H., Nishio, H., Zielinski, R., and Dugaiczyk, A. (1999) Origin and phylogenetic distribution of Alu DNA repeats: Irreversible events in the evolution of primates. J. Mol. Biol. 289, 861-871.
18. Hirano, H., Mochizuki, K., Umeda, M., Ohtsubo, H., Ohtsubo, E., and Sano, Y. (1994) Retrotransposition of a plant SINE into the wx locus during evolution of rice. J. Mol. Evol. 38, 132-137.
19. Ishii, T., Nakano, T., Maeda, H., and Kamijima, O. (1996) Phylogenetic relationships in A-genome species of rice as revealed by RAPD analysis, Genes Genet. Syst. 71, 195-201.
20. Khush, G. S. (1997) Origin, dispersal, cultivation and variation of rice. Plant Mol. Biol, 35, 25-34.
21. Li, H. W., Chen, C. C., Wu, H. K., and Lu, K. C. L. (1964) Studies on genetic and cytogenetic evidence for species relationships in the Republic of China. In: Rice Genetics and Cytogenetics, pp. 118-131. IRRI, Elsevier, Amsterdam.
22. Maraia, R. J. (1995) The Impact of Short Interspersed Elements (SINEs) on the Host Genome. Springer, New York, NY.
23. Mochizuki, K., Umeda, M., Ohtsubo, H., and Ohtsubo, E. (1992) Characterization of a plant SINE, p-SINE1, in rice genomes. Jpn. J. Genet. 67, 155-166.
24. Mochizuki, K., Ohtsubo, H., Hirano, H., Sano, Y., and Ohtsubo, E. (1993) Classification and relationships of rice strains with AA genome by identification of transposable elements at nine loci. Jpn. J. Genet. 68, 205-217.
25. Morinaga, T. (1964) Cytogenetical investigation on Oryza species.In: Rice Genetics and Cytogenetics, pp. 91-103. IRRI, Elsevier, Amsterdam.
26. Morishima, H. (1969) Phenetic similarity and phylogenetic relationships among strains of Oryza perennis, estimated by methods of numerical taxonomy. Evolution 23, 429-443
27. Morishima, H., Sano, Y., and Oka, H. I. (1992) Evolutionary studies in cultivated rice and its wild relatives. Oxford Surveys Evol. Biol. 8, 135-184.
28. Motohashi, R., Mochizuki, K., Ohtsubo, H., and Ohtsubo, E. (1997) Structures and distribution of p-SINE1 members in rice genomes. Theor. Appl. Genet. 95, 359-368.
29. Murata, S., Takasaki, N., Saitoh, M., and Okada, N. (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.
30. Naredo, M. E. B., Juliana, A. B., Lu, B. R., and Jackson, M. T. (1998) Taxonomic status of Oryza glumaepatula Steud. II. Hybridization between new world diploids and AA-genome species from Asia and Australia. Genet. Resour. Crop Evol. 45, 205-214.
31. Nikaido, M., Rooney, A. P., and Okada, N. (1999) Phylogenetic relationships among cetartiodactyls based on insertions of short and long interspersed elements: Hippopotamuses are the closest extant relatives of whales. Proc. Natl. Acad. Sci. USA 96, 10261-10266.
32. Second, G. (1985) Evolutionary relationships in the Sativa group of Oryza based on isozyme data. Génét. Sél. Evol. 17, 89-114.
33. Shedlock, A. M., and Okada, N. (2000) SINE insertions: Powerful tools for molecular systematics. BioEssays 22, 148-160.
34. Shimamura, M., Yasue, H., Ohshima, K., Abe, H., Kato, H., Kishiro, T., Goto, M., Munechika, I., and Okada, N. (1997) Molecular evidence from retroposons that whales form a clad within even-toed ungulates. Nature 388, 666-670.
35. Smith, T. F., and Waterman, M. S. (1981) Identification of common molecular subsequences. J. Mol. Biol. 147, 195-197.
36. Spertini, D., Beliveau, C., and Bellemare, G. (1999) Screening of transgenic plants by amplification of unknown genomic DNA flanking T-DNA. Biotechniques 27, 308-314.
37. Swofford, D. L. (1998) PAUP*. Phylogenetic Analysis Using Parsimony (*and Other Methods). Version 4. Sinauer, Sunderland, Massachusetts.
38. Takahashi, K., Terai, Y., Nishida, M., and Okada, N. (1998) A novel family of short interspersed repetitive elements (SINEs) from cichilds: The pattern of insertion of SINEs at orthologous loci support the proposed monophyly of four major groups of cichild fishes in Lake Tanganyika. Mol. Biol. Evol. 15, 391-407.
39. Tanksley, S. D., and McCouch, S. R. (1997) Seed banks and molecular maps: Unlocking genetic potential from the wild. Science 277, 1063-1066.
40. Tatout, C., Warwick, S., Lenoir, A., and Deragon, J. M. (1999) SINE insertions as clade markers for wild crucifers species. Mol. Biol. Evol. 16, 1614-1621.
41. Tenzen, T., Matsuda, Y., Ohtsubo, H., and Ohtsubo, E. (1994) Transposition of Tnr1 in rice genomes to 5′-PuTAPy-3′ sites, duplicating the TA sequence. Mol. Gen. Genet. 245, 441- 448.
42. Umeda, M., Ohtsubo, H., and Ohtsubo, E. (1991) Diversification of the rice Waxy gene by insertion of mobile DNA elements into introns. Jpn. J. Genet. 66, 569-586.
43. Vaughan, D. A. 1994. The Wild Relatives of Rice: A Genetic Resources Handbook. International Rice Research Institute, Philippines.
44. Wang, Z. Y., Second, G., and Tanksley, S. D. (1992) Polymorphism and phylogenetic relationships among species in the genus Oryza as determined by analysis of nuclear RFLPs. Theor. Appl. Genet. 83, 565-581.
45. Wu C.-I. (1991) Inference of species phylogeny in relation to segregation of ancient polymorphism. Genetics 127, 429-435.