Sources and predictors of resolvable indel polymorphism assessed using rice as a model

Molecular Genetics and Genomics

Volumn 271, Issue 3, 2004, Pages 298-307

  Edwards, J D ^a   LeeV M , ^a   McCouch, S R ^a  

^a Department of Obstetrics Gynecology   (United States)

Author keywords

Insertions Deletions (Indels); Oryza sativa L.; Restriction Fragment Length Polymorphisms (RFLPS); Rice; Transposable elements

Indexed keywords

ANALYTIC METHOD; ARTICLE; DNA METHYLATION; DNA POLYMORPHISM; GENE DELETION; GENE INSERTION; LONG TERMINAL REPEAT; MOLECULAR MODEL; MOLECULAR RECOGNITION; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; RESTRICTION FRAGMENT LENGTH POLYMORPHISM; RICE; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS;

DNA TRANSPOSABLE ELEMENTS; DNA, PLANT; GENE FREQUENCY; GENES, PLANT; GENETIC MARKERS; GENOTYPE; MODELS, GENETIC; ORYZA SATIVA; POLYMORPHISM, GENETIC; POLYMORPHISM, RESTRICTION FRAGMENT LENGTH; REPETITIVE SEQUENCES, NUCLEIC ACID; SEQUENCE ANALYSIS, DNA; SEQUENCE DELETION; VARIATION (GENETICS);

ACARI; ARABIDOPSIS; JAPONICA; ORYZA SATIVA;

EID: 2342582058     PISSN: 16174615     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00438-004-0979-7     Document Type: Article

References (36)

1. Akagi H, Yokozeki Y, Inagaki A, Mori K, Fujimura T (2001) Micron, a microsatellite-targeting transposable element in the rice genome. Mol Genet Genomics 266:471-480
2. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215:403-410
3. Bernaola-Galvan P, Roman-Roldan R, Oliver JL (1996) Compositional segmentation and long-range fractal correlations in DNA sequences. Physical Rev E. Statistical Physics, Plasmas, Fluids, and Related Interdisciplinary Topics 53:5181-5189
4. Bird AP (1980) DNA methylation and the frequency of CpG in animal DNA. Nucleic Acids Res 8:1499-1504
5. Bishop DT, Williamson JA, Skolnick MH (1983) A model for restriction fragment length distributions. Am J Hum Genet 35:795-815
6. Botstein D, White RL, Skolnick M, Davis RW (1980) Construction of a genetic linkage map in man using restriction fragment length polymorphisms. Am J Hum Genet 32:314-331
7. Bureau TE, Wessler SR (1992) Tourist: a large family of small inverted repeat elements frequently associated with maize genes. Plant Cell 4:1283-1294
8. Bureau TE, Ronald PC, Wessler SR (1996) A computer-based systematic survey reveals the predominance of small inverted-repeat elements in wild-type rice genes. Proc Natl Acad Sci USA 93:8524-8529
9. Feng Q, et al (2002) Sequence and analysis of rice chromosome 4. Nature 420:316-320
10. Houck CM, Rinehart FP, Schmid CW (1979) A ubiquitous family of repeated DNA sequences in the human genome. J Mol Biol 132:289-306
11. Innan H, Terauchi R, Kahl G, Tajima F (1999) A method for estimating nucleotide diversity from AFLP data. Genetics 151:1157-1164
12. Jaccoud D, Peng K, Feinstein D, Kilian A (2001) Diversity arrays: a solid state technology for sequence information independent genotyping. Nucleic Acids Res 29:E25
13. Jiang N, Bao Z, Zhang X, Hirochika H, Eddy SR, McCouch SR, Wessler SR (2003) An active DNA transposon family in rice. Nature 421:163-167
14. Kidwell MG (1983) Evolution of hybrid dysgenesis determinants in Drosophila melanogaster. Proc Natl Acad Sci USA 80:1655-1659
15. Kikuchi K, Terauchi K, Wada M, Hirano HY (2003) The plant MITE mPing is mobilized in anther culture. Nature 421:167-170
16. Kunz M, Radl Z (1998) Distributions of distances in information strings. J Chem Inf Comput Sci 38:374-378
17. Lenoir A, Lavie L, Prieto JL, Goubely C, Cote JC, Pelissier T, Deragon JM (2001) The evolutionary origin and genomic organization of SINEs in Arabidopsis thaliana. Mol Biol Evol 18:2315-2322
18. Lindroth AM, Cao X, Jackson JP, Zilberman D, McCallum CM, Henikoff S, Jacobsen SE (2001) Requirement of CHROMOMETHYLASE3 for maintenance of CpXpG methylation. Science 292:2077-2080
19. Mao L, Wood TC, Yu Y, Budiman MA, Tomkins J, Woo S, Sasinowski M, Presting G, Frisch D, Goff S, Dean RA, Wing RA (2000) Rice transposable elements: a survey of 73,000 sequence-tagged-connectors. Genome Res 10:982-990
20. Matsuoka Y, Vigouroux Y, Googmann MM, Sanchez GJ, Buckler E, Doebley J (2002) A single domestication for maize shown by multilocus microsatellite genotyping. Proc Natl Acad Sci USA 99:6080-6084
21. McCarthy EM, Liu J, Lizhi G, McDonald JF (2002) Long terminal repeat retrotransposons of Oryza sativa. Genome Biol 3:research0053.1-0053.11
22. McCouch SR, Kochert G, Yu ZH, Wang ZY, Khush GS (1988) Molecular mapping of rice chromosomes. Theor Appl Genet 76:815-829
23. Mochizuki K, Ohtsubo H, Hirano H, Sano Y, 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
24. Myers EW, Miller W (1988) Optimal alignments in linear space. Comput Appl Biosci 4:11-7
25. Nagano H, Kunii M, Azuma T, Kishima Y, Sano Y (2002) Characterization of the repetitive sequences in a 200-kb region around the rice waxy locus: diversity of transposable elements and presence of veiled repetitive sequences. Genes Genet Syst 77:69-79
26. Nakazaki T, Okumoto Y, Horibata A, Yamahira S, Teraishi M, Nishida H, Inoue H, Tanisaka T (2003) Mobilization of a transposon in the rice genome. Nature 421:170-172
27. Nei M, Miller JC (1990) A simple method for estimating average number of nucleotide substitutions within and between populations from restriction data. Genetics 125:873-879
28. Rice P, Longden I, Bleasby A (2000) EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet 16:276-277
29. Roberts RJ, Vincze T, Posfai J, Macelis D (2003) REBASE: restriction enzymes and methyltransferases. Nucleic Acids Res 31:418-420
30. SanMiguel P, Gaut BS, Tikhonov A, Nakajima Y, Bennetzen JL (1998) The paleontology of intergene retrotransposons of maize. Nat Genet 20:43-45
31. Second G (1982) Origin of the gene diversity of cultivated rice ( Oryza sativa L.): study of the polymorphism scored at 40 isoenzyme loci. Jpn J Genet 57:25-57
32. Tarchini R, Biddle P, Wineland R, Tingey S, Rafalski A (2000) The complete sequence of 340 kb of DNA around the rice Adh1-adh2 region reveals interrupted colinearity with maize chromosome 4. Plant Cell 12:381-391
33. Turcotte K, Srinivasan S, Bureau T (2001) Survey of transposable elements from rice genomic sequences. Plant J 25:169-179
34. Upholt WB (1977) Estimation of DNA divergence from comparison of restriction endonuclease digests. Nucleic Acids Res 4:1257-1265
35. Vos P, Hogers R, Bleeker M, Reijans M, van de Lee T, Hornes M, Frijters A, Pot J, Peleman J, Kuiper M, Zabeau M (1995) AFLP: a new technique for DNA fingerprinting. Nucleic Acids Res 23:4407-4414
36. Voss RF (1992) Evolution of long-range fractal correlations and I/f noise in DNA base sequences. Phys Rev Lett 68:3805-3808