Polyphyletic origin of cultivated rice: Based on the interspersion pattern of SINEs

Molecular Biology and Evolution

Volumn 20, Issue 1, 2003, Pages 67-75

  Cheng, Chaoyang ^a   Motohashi, Reiko ^a,c   Tsuchimoto, Suguru ^a   Fukuta, Yoshimichi ^b   Ohtsubo, Hisako ^a   Ohtsubo, Eiichi ^a  

^a UNIVERSITY OF TOKYO   (Japan)

^b Hokuriku Natl Agr Expt Stn   (Japan)

^c RIKEN TSUKUBA INSTITUTE   (Japan)

Author keywords

Indica and japonica rice; Insertion polymorphism; Oryza rufipogon; Oryza sativa; Polyphyletic origin; SINE

Indexed keywords

ARTICLE; CLASSIFICATION; CONTROLLED STUDY; DNA POLYMORPHISM; GENE INSERTION; NONHUMAN; PHYLOGENY; POLYPHYLY; RETROPOSON; RICE; SHORT INTERSPERSED REPEAT; STRAIN DIFFERENCE; TAXONOMY;

ANIMALS; BASE SEQUENCE; CROPS, AGRICULTURAL; GENES, PLANT; GENOME; HUMANS; MOLECULAR SEQUENCE DATA; ORYZA SATIVA; PHYLOGENY; POLYMORPHISM, GENETIC; SEQUENCE ALIGNMENT; SHORT INTERSPERSED NUCLEOTIDE ELEMENTS;

EMBRYOPHYTA; JAPONICA; ORYZA RUFIPOGON; ORYZA SATIVA; ZIZANIA;

EID: 0037225254     PISSN: 07374038     EISSN: None     Source Type: Journal    
DOI: 10.1093/molbev/msg004     Document Type: Article

References (50)

1. Altschul, S. F., W. Gish, W. Miller, E. W. Myers, and D. J. Lipman. 1990. Basic local alignment search tool. J. Mol. Biol. 215:403-410.
2. Bailey, A. D., and C. K. J. Shen. 1993. Sequential insertion of Alu family repeats into specific genomic sites of higher primates. Proc. Natl. Acad. Sci. USA 90:7205-7209.
3. -. 1997. Molecular origin of the mosaic sequence arrangements of higher primate a-globin duplication units. Proc. Natl. Acad. Sci. USA 94:5177-5182.
4. Batzer, M. A., M. Stoneking, M. Alegria-Hartman et al. (11 co-authors). 1994. African origin of human-specific polymorphic Alu insertions. Proc. Natl. Acad. Sci. USA 91:12288-12292.
5. Chang, T.-T. 1976. The origin, evolution, cultivation, disseminationand diversification of Asian and African rice. Euphytica 25:425-441.
6. Cheng, C., S. Tsuchimoto, H. Ohtsubo, and E. Ohtsubo. 2002. Evolutionary relationships among rice species with AA genome based on SINE insertion analysis. Genes Genet. Syst. 77:323-334.
7. Dally, A. M., and G. Second. 1990. Chloroplast DNA diversity in wild and cultivated species of rice (Genus Oryza, section Oryza): cladistic-mutation and genetic-distance analysis. Theor. Appl. Genet. 80:209-222.
8. Glaszmann, J. C. 1987. Isozymes and classification of Asian rice varieties. Theor. Appl. Genet. 74:21-30.
9. Hamada, M., N. Takasaki, J. D. Reist, A. L. Decicco, A. Goto, and N. Okada. 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.
10. Hamdi, H., H. Nishio, R. Zielinski, and A. Dugaiczyk. 1999. Origin and phylogenetic distribution of Alu DNA repeats: irreversible events in the evolution of primates. J. Mol. Biol. 289:861-871.
11. Hirano, H.-Y., K. Mochizuki, M. Umeda, H. Ohtsubo, E. Ohtsubo, and Y. Sano. 1994. Retrotransposition of a plant SINE into the wx locus during evolution of rice. J. Mol. Evol. 38:132-137.
12. Kaneda, C., M. Umikawa, M. R. Singh, C. Nakamura, and N. Mori. 1996. Genetic diversity and subspecies differentiation in local rice cultivars from Manipur state of India. Breed. Sci. 46:159-166.
13. Kanno, A., N. Watanabe, I. Nakamura, and A. Hirai. 1993. Variations in chloroplast DNA from rice (Oryza sativa): differences between deletions mediated by short direct-repeat sequences within a single species. Theor. Appl. Genet. 86:579-584.
14. Kato, S., H. Kosaka, and S. Hara. 1928. On the affinity of rice varieties as shown by fertility of hybrid plants (in Japanese). Bull. Sci. Fac. Agric. Kyushu Univ. 3:132-147.
15. Khush, G. S. 1997. Origin, dispersal, cultivation and variation of rice. Plant Mol. Biol. 35:25-34.
16. Maraia, R. J. 1995. The impact of short interspersed elements (SINEs) on the host genome. Springer-Verlag, New York.
17. Matsuo, T. 1952. Genealogical studies on cultivated rice (in Japanese). Bull. Natl. Inst. Agric. Sci. Jpn. 3:1-111.
18. Mochizuki, K., H. Ohtsubo, H. Hirano, Y. Sano, and E. Ohtsubo. 1993. Classification and relationships of rice strains with AA genome by identification of transposable elements at nine loci. Jpn. J. Genet. 68:205-217.
19. Mochizuki, K., M. Umeda, H. Ohtsubo, and E. Ohtsubo. 1992. Characterization of a plant SINE, p-SINE1, in rice genomes. Jpn. J. Genet. 67:155-166.
20. Morinaga, T. 1954. Classification of rice varieties on the basis of affinity. Pp. 1-14 in Reports of the 5th Meeting of the International Rice Commission's Working Party on Rice Breeding. Ministry of Agriculture and Forestry, Tokyo.
21. Morishima, H. 1986. Wild progenitors of cultivated rice and their population dynamics. Pp. 3-14 in Rice genetics. International Rice Research Institute, Manila.
22. Morishima, H., H. I. Oka, and W.-T. Chang. 1961. Directions of differentiation in populations of wild rice, Oryza perennis and O. sativa F. spontanea. Evolution 15:326-339.
23. Morishima, H., Y. Sano, and H. I. Oka. 1984. Differentiation of perennial and annual types due to habitat conditions in the wild rice Oryza perennis. Plant Syst. Evol. 144:119-135.
24. -. 1992. Evolutionary studies in cultivated rice and its wild relatives. Oxford Surveys Evol. Biol. 8:135-184.
25. Motohashi, R., K. Mochizuki, H. Ohtsubo, and E. Ohtsubo. 1997. Structures and distribution of p-SINE1 members in rice genomes. Theor. Appl. Genet. 95:359-368.
26. 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.
27. Nikaido, M., A. P. Rooney, and N. Okada. 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.
28. Ohtsubo, H., M. Umeda, and E. Ohtsubo. 1991. Organization of DNA sequences highly repeated in tandem in rice genomes. Jpn. J. Genet. 66:241-254.
29. Oka, H. I. 1958. Intervarietal variation and classification of cultivated rice. Indian J. Genet. Plant Breed. 18:79-89.
30. -. 1964. Pattern of interspecific relationships and evolutionary dynamics in Oryza. Pp. 71-90 in Rice genetics and cytogenetics. International Rice Research Institute, Elsevier, Amsterdam.
31. -. 1974. Experimental studies on the origin of cultivated rice. Genetics 78:475-486.
32. -. 1988. Origin of cultivated rice. Japan Sci. Soc. Press/Elsevier, Tokyo/Amsterdam.
33. Oka, H. I., and Morishima, H. 1967. Variations in the breeding systems of a wild rice, Oryza perennis. Evolution 21:249-258.
34. -. 1982. Phylogenetic differentiation of cultivated rice. XXIII. Potentiality of wild progenitors to evolve the indica and japonica types of rice cultivars. Euphytica 31:41-50.
35. Roy, A. M., M. L. Carroll, D. H. Kass, S. V. Nguyen, A.-H. Salem, M. A. Batzer, and P. L. Deininger. 1999. Recently integrated human Alu repeats: finding needles in the haystack. Genetica 107:149-161.
36. Sano, Y., H. Morishima, and H. I. Oka. 1980. Intermediate perennial-annual populations of Oryza perennis found in Thailand and their evolutionary significance. Bot. Mag. (Tokyo) 93:291-305.
37. Second, G. 1982. Origin of the genic diversity of cultivated rice (Oryza spp.): study of the polymorphism scored at 40 isozyme loci. Jpn. J. Genet. 57:25-57.
38. Sharma, S. D., and S. V. S. Shastry. 1965. Taxonomic studies in genus Oryza L: III. O. rufipogon griff. sensu stricto and O. nivara Sharma et Shastry nom. nov. Indian J. Genet. Plant Breed. 25:157-167.
39. Shedlock, A. M., and N. Okada. 2000. SINE insertions: powerful tools for molecular systematics. BioEssays 22:148-160.
40. Shimamura, M., H. Yasue, K. Ohshima, H. Abe, H. Kato, T. Kishiro, M. Goto, I. Munechika, and N. Okada. 1997. Molecular evidence from retroposons that whales form a clad within even-toed ungulates. Nature 388:666-670.
41. Smith, T. F., and M. S. Waterman. 1981. Identification of common molecular subsequences. J. Mol. Biol. 147:195-197.
42. Spertini, D., C. Beliveau, and G. Bellemare. 1999. Screening of transgenic plants by amplification of unknown genomic DNA flanking T-DNA. Biotechniques 27:308-314.
43. Swofford, D. L. 1998. PAUP*: phylogenetic analysis using parsimony (*and other methods). Version 4. Sinauer Associates, Sunderland, Mass.
44. Takasaki, N., T. Yamaki, M. Hamada, L. Park, and N. Okada. 1997. 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 146:369-380.
45. Tatout, C., S. Warwick, A. Lenoir, and J. M. Deragon. 1999. SINE insertions as clade markers for wild crucifers species. Mol. Biol. Evol. 16:1614-1621.
46. Tenzen, T., Y. Matsuda, H. Ohtsubo, and E. Ohtsubo. 1994. Transposition of Tnr1 in rice genomes to 5′-PuTAPy-3′ sites, duplicating the TA sequence. Mol. Gen. Genet. 245:441-448.
47. Umeda, M., H. Ohtsubo, and E. Ohtsubo. 1991. Diversification of the rice Waxy gene by insertion of mobile DNA elements into introns. Jpn. J. Genet. 66:569-586.
48. Wang, Z. Y., and S. D. Tanksley. 1989. Restriction fragment length polymorphism in Oryza sativa L. Genome 32:1113-1118.
49. Wang, Z. Y., G. Second, and S. D. Tanksley. 1992. Polymorphism and phylogenetic relationships among species in the genus Oryza as determined by analysis of nuclear RFLPs. Theor. Appl. Genet. 83:565-581.
50. Wu, C.-I. 1991. Inference of species phylogeny in relation to segregation of ancient polymorphism. Genetics 127:429-435.