Long terminal repeat retrotransposons of Oryza sativa

Genome Biology

Volumn 3, Issue 10, 2002, Pages

  McCarthy, Eugene M ^a   Liu, Jingdong ^b   Lizhi, Gao ^a   McDonald, John F ^a  

^a University of Georgia ^*  (United States)

^b MONSANTO COMPANY   (United States)

Author keywords

Long Terminal Repeat; Long Terminal Repeat Retrotransposons; Reverse Transcriptase Sequence; Rice Genome; Total Copy Number

Indexed keywords

ANIMAL; ARTICLE; BIOLOGY; CONFORMATION; GENE; GENE DOSAGE; GENETIC DATABASE; GENETICS; LONG TERMINAL REPEAT; METHODOLOGY; MULTIGENE FAMILY; RETROPOSON; RICE; SEQUENCE HOMOLOGY;

ANIMALS; COMPUTATIONAL BIOLOGY; DATABASES, GENETIC; GENE DOSAGE; GENES, INSECT; GENES, PLANT; MULTIGENE FAMILY; NUCLEIC ACID CONFORMATION; ORYZA SATIVA; RETROELEMENTS; SEQUENCE HOMOLOGY, NUCLEIC ACID; TERMINAL REPEAT SEQUENCES;

EID: 0037072652     PISSN: 14747596     EISSN: 1474760X     Source Type: Journal    
DOI: 10.1186/gb-2002-3-10-research0053     Document Type: Article

References (33)

1. SanMiguel P, Tikhanov A, Jin YK, Motchoulskaia N, Zakharov D, Melake-Berhan A, Springer PS, Edwards KJ, Lee M, Avramova Z, Bennetzen JL: Nested retrotransposons in the intergenic regions of the maize genome. Science. 1996, 274: 765-768. 10.1126/science.274.5288.765. DOI: 10.1126/science.274.5288.765
2. Flavell RB: Repetitive DNA and chromosome evolution in plants. Philos Trans R Soc Lond B Biol Sci. 1986, 312: 227-242. DOI: 10.1098/rstb.1986.0004
3. Yoder JA, Walsh CP, Bestor TH: Cytosine methylation and the ecology of intragenomic parasites. Trends Genet. 1997, 13: 335-340. 10.1016/S0168-9525(97)01181-5. DOI: 10.1016/S0168-9525(97)01181-5
4. Smit AF: Interspersed repeats and other mementos of transposable elements in mammalian genomes. Curr Opin Genet Dev. 1999, 9: 657-663. 10.1016/S0959-437X(99)00031-3. DOI: 10.1016/S0959-437X(99)00031-3
5. Arumuganathan K, Earle ED: Nuclear DNA content of some important plant species. Plant Mol Biol Rep. 1991, 9: 208-218. DOI: 10.1007/BF02672069
6. Plant DNA C-values database. [http://www.rbgkew.org.uk/cval/searchguide.html]
7. Bowen N, McDonald JF: Drosophila euchromatic LTR retrotransposons are much younger than the host species in which they reside. Genome Res. 2000, 11: 1527-1540. 10.1101/gr.164201. DOI: 10.1101/gr.164201
8. Hirochika H, Fukuchi A, Kikuchi F: Retrotransposon families in rice. Mol Gen Genet. 1992, 233: 209-216. DOI: 10.1007/BF00587581
9. Nakajima R, Noma K, Ohtsubo H, Ohtsubo E: Identification and characterization of two tandem repeat sequences (TrsB and TrsC) and a retrotransposon (Rire1) as genome-general sequences in rice. Genes Genet Syst. 1996, 71: 373-382. DOI: 10.1266/ggs.71.373
10. Bowen N, McDonald JF: Genomic analysis of Caenorhabditis elegans reveals ancient families of retroviral-like elements. Genome Res. 1999, 9: 924-935. 10.1101/gr.9.10.924. DOI: 10.1101/gr.9.10.924
11. Burns DP, Temin HM: High rates of frameshift mutations within homo-oligomeric runs during a single cycle of retroviral replication. J Virol. 1994, 68: 4196-4203.
12. SanMiguel P, Gaut BS, Tikhonov A, Nakajima Y, Bennetzen JL: The paleontology of intergene retrotransposons of maize. Nat Genet. 1998, 20: 43-45. 10.1038/1695. DOI: 10.1038/1695
13. Turcotte K, Srinivasan S, Bureau T: Survey of transposable elements from rice genomic sequences. Plant J. 2001, 25: 169-180. 10.1046/j.1365-313x.2001.00945.x. DOI: 10.1046/j.1365-313x.2001.00945.x
14. Wang SP, Liu N, Peng KM, Zhang QF: The distribution and copy number of copia-like retrotransposons in rice (Oryza sativa L.) and their implications in the organization and evolution of the rice genome. Proc Natl Acad Sci USA. 1999, 96: 6824-6828. 10.1073/pnas.96.12.6824. DOI: 10.1073/pnas.96.12.6824
15. Mao L, Wood TC, Yu Y, Budiman MA, Tomkins J, Woo S, Sasinowski M, Presting G, Frisch D, Goff S, et al: Rice transposable elements: a survey of 73,000 sequence-tagged-connectors. Genome Res. 2000, 10: 982-990. 10.1101/gr.10.7.982. DOI: 10.1101/gr.10.7.982
16. Tarchini R, Biddle P, Wineland R, Tingey S, Rafalski A: The complete sequence of 340 kb of DNA around the rice Adh1-Adh2 region reveals interrupted co-linearity with maize chromosome 4. Plant Cell. 2000, 12: 381-392. 10.1105/tpc.12.3.381. DOI: 10.1105/tpc.12.3.381
17. Heslop-Harrison JS, Brandes A, Taketa S, Schmidt T, Vershinin AV, Alkhimova EG, Karum A, Doudrick RL, Scwarzacher T, Katsiotis A, et al: The chromosomal distributions of Ty1-copia group retrotransposable elements in higher plants and their implications for genome evolution. Genetica. 1997, 100: 197-204. 10.1023/A:1018337831039. DOI: 10.1023/A:1018337831039
18. Boeke JD, Stoye JP: Retrotransposons, endogenous retroviruses and the evolution of retroviruses. In Retroviruses,. Edited by: Coffin J, Hughes S, Varmus H. 1997, Cold Spring Harbor, NY: Cold Spring Harbor Laboratory Press;, 343-435.
19. Jordan IK, McDonald JF: Tempo and mode of evolution in Saccharomyces cerevisiae genome. Genetics. 1999, 151: 1341-1351.
20. Promislow DE, Jordan IK, McDonald JF: Genomic demography: A life history analysis of transposable element evolution. Proc R Soc Lond B Biol Sci. 1999, 266: 1555-1560. 10.1098/rspb.1999.0815. DOI: 10.1098/rspb.1999.0815
21. Kapitonov VV, Jurka J: Molecular paleontology of transposable elements from Arabidopsis thaliana. Genetica. 1999, 107: 27-37. 10.1023/A:1004030922447. DOI: 10.1023/A:1004030922447
22. Tristem M: Identification and characterization of novel human endogenous retrovirus families by phylogenetic screening of the human genome mapping project database. J Virol. 2000, 74: 3715-3730. 10.1128/JVI.74.8.3715-3730.2000. DOI: 10.1128/JVI.74.8.3715-3730.2000
23. Hirochika H, Sugimoto K, Otsuki Y, Tsugawa H, Kanda M: Retrotransposons of rice involved in mutations induced by tissue culture. Proc Natl Acad Sci USA. 1996, 93: 7783-7788. 10.1073/pnas.93.15.7783. DOI: 10.1073/pnas.93.15.7783
24. Noma K, Nakajima R, Ohtsubo H, Ohtsubo E: Rire1, a retrotransposon from wild rice Oryza australiensis. Genes Genet Syst. 1997, 72: 131-40. 10.1266/ggs.72.131. DOI: 10.1266/ggs.72.131
25. Kumekawa N, Ohtsubo H, Horiuchi T, Ohtsubo E: Identification and characterization of novel retrotransposons of the gypsy type in rice. Mol Gen Genet. 1999, 260: 593-602. 10.1007/s004380050933. DOI: 10.1007/s004380050933
26. Li ZY, Chen SY, Zheng XW, Zhu LH: Identification and chromosomal localization of a transcriptionally active retrotransposon of Ty3-gypsy type in rice. Genome. 2000, 43: 404-408. 10.1139/gen-43-2-404. DOI: 10.1139/g99-137
27. Kumar A, Bennetzen JL: Plant retrotransposons. Ann Rev Genet. 1999, 33: 479-532. 10.1146/annurev.genet.33.1.479. DOI: 10.1146/annurev.genet.33.1.479
28. Wendel JF, Wessler SR: Retrotransposon-mediated genome evolution on a local ecological scale. Proc Natl Acad Sci USA. 2000, 97: 6250-6252. 10.1073/pnas.97.12.6250. DOI: 10.1073/pnas.97.12.6250
29. Witte CP, Le QH, Bureau T, Kumar A: Terminal-repeat retrotransposons in miniature (TRIM) are involved in restructuring plant genomes. Proc Natl Acad Sci USA. 2001, 98: 13778-83. 10.1073/pnas.241341898. DOI: 10.1073/pnas.241341898
30. The Institute for Genomic Research rice gene index. [http://www.tigr.org/tdb/ogi/.]
31. Xiong Y, Eickbush TH: Similarity of reverse transcriptase-like sequences of viruses, transposable elements, and mitochondrial introns. Mol Biol Evol. 1988, 5: 675-690.
32. Xiong Y, Eickbush TH: Origin and evolution of retroelements based upon their reverse-transcriptase sequences. EMBO J. 1990, 9: 3353-3362.
33. Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG: The CLUSTAL X windows interface: Flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res. 1997, 25: 4876-4882. 10.1093/nar/25.24.4876. DOI: 10.1093/nar/25.24.4876