Evolutionary history of Oryza sativa LTR retrotransposons: A preliminary survey of the rice genome sequences

BMC Genomics

Volumn 5, Issue , 2004, Pages

  Gao, Lizhi ^a   McCarthy, Eugene M ^a   Ganko, Eric W ^a   McDonald, John F ^a  

^a University of Georgia ^*  (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CHROMOSOME 10; COMPUTER ANALYSIS; DATA BASE; GENE SEQUENCE; GENOME ANALYSIS; LONG TERMINAL REPEAT; MOLECULAR EVOLUTION; NONHUMAN; NUCLEOTIDE SEQUENCE; PLANT AGE; PLANT CHROMOSOME; PLANT GENETICS; RETROPOSON; RICE; SEQUENCE ANALYSIS; SPECIES;

CHROMOSOMES, PLANT; EVOLUTION, MOLECULAR; GENES, PLANT; GENETIC VARIATION; GENOME, PLANT; MUTAGENESIS, INSERTIONAL; ORYZA SATIVA; PHYLOGENY; RETROELEMENTS; TERMINAL REPEAT SEQUENCES; TIME FACTORS;

EUKARYOTA; ORYZA SATIVA;

EID: 2442657861     PISSN: 14712164     EISSN: None     Source Type: Journal    
DOI: 10.1186/1471-2164-5-18     Document Type: Article

References (48)

1. Berg DE, Howe MM: Mobile DNA Washington, DC: American Society for Microbiology; 1989.
2. Voytas DF, Boeke JD: Yeast retrotransposon revealed. Nature 1992, 358:717.
3. Suoniemi A, Tanskanen J, Pentikainen O, Johnson MS, Schulman AH: The core domain of retrotransposon integrase in Hordeum: predicted structure and evolution. Mol Biol Evol 1998, 15:1135-44.
4. Kumar A, Bennetzen JL: Plant retrotransposons. Annu Rev Genet 1999, 33:479-532.
5. SanMiguel P, Tikhonov 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.
6. Flavell RB: Repetitive DNA and chromosome evolution in plants. Philos Trans R Soc Lond B Biol Sci 1986, 312:227-242.
7. McDonald JF: Evolution and consequences of transposable elements. Curr Opin Genet Dev 1993, 3:855-864.
8. McDonald JF: Transposable elements: Possible catalysts of organismic evolution. Trends Ecol Evol 1995, 10:123-126.
9. McDonald JF: Transposable elements and genome evolution Boston, MA: Kluewer Academic Press; 1995.
10. Britten RJ: Mobile elements inserted in the distant past have taken on important functions. Gene 1997, 205:177-182.
11. Brosius J: RNAs from all categories generate retrosequences that may be exapted as novel genes or regulatory elements. Gene 1999, 238:115-134.
12. Kidwell MG, Lisch DR: Transposable elements and host genome evolution. Trends Ecol Evol 2000, 15:95-99.
13. Feschotte C, Jiang N, Wessler SR: Plant transposable elements: where genetics meets gemomics. Nature Reviews Genetics 2002, 3:329-341.
14. Arumuganathan K, Earle ED: Nuclear DNA content of some important plant species. Plant Mol Biol Rep 1991, 9:208-218.
15. Sasaki T, Burr B: International rice genome sequencing project: The effort to completely sequence the rice genome. Curr Opin Plant Biol 2000, 3:138-141.
16. Gale MD, Devos KM: Comparative genetics in the grasses. Proc Natl Acad Sci 1998, 95:1971-1974.
17. 2 population. Genetics 1998, 148:479-494.
18. Cheng ZK., Buell CR, Wing RA, Gu MH, Jiang JM: Toward a Cytological Characterization of the Rice Genome. Genome Res 2001, 11:2133-2141.
19. Hiei Y, Ohta T, Komari T, Kumashiru T: Efficient transformation of rice (Oryza sativa L.) mediated by Agrobacterium and sequence analysis of the boundaries of the T-DNA. Plant J 1994, 6:271-282.
20. Yamamoto K, Sasaki T: Large-scale EST Sequencing in Rice. Plant Mol Biol 1997, 35:135-144.
21. Jackson MT: Conservation of rice genetic resources: the role of the International Rice Genebank at IRRI. Pl Mol Biol 1997, 35:61-67.
22. Yu J, Hu S, Wang J, Wong GK-S, Li S, Liu B, Deng Y, Dai L, Zhou Y, Zhang X, Cao M, Liu J, Sun J, Tang J, Chen Y, Huang X, Lin W, Ye C, Tong W, Cong L, Geng J, Han Y, Li L, Li W, Hu G, Huang X, Li W, Li J, Liu Z, Li L, Liu J, Qi Q, Liu J, Li L, Li T, Wang X, Lu H, Wu T, Zhu M, Ni P, Han H., Dong W, Ren X, Feng X, Cui P, Li X, Wang H, Xu X, Zhai W, Xu Z, Zhang J, He S, Zhang J, Xu J, Zhang K, Zheng X, Dong J, Zeng W, Tao L, Ye J, Tan J, Ren X, Chen X, He J, Liu D, Tian W, Tian C, Xia H, Bao Q, Li G, Gao H, Cao T, Wang J, Zhao W, Li P, Chen W, Wang X, Zhang Y, Hu J, Wang J, Liu S, Yang J, Zhang G, Xiong Y, Li Z, Mao L, Zhou C, Zhu Z, Chen R, Hao B, Zheng W, Chen S, Guo W, Li G, Liu S, Tao M, Wang J, Zhu L, Yuan L, Yang H: A Draft Sequence of the Rice Genome (Oryza sativa L. ssp. indica). Science 2002, 296:79-92.
23. Goff SA, Ricke D, Lan TH, Presting G, Wang R, Dunn M, Glazebrook J, Sessions A, Oeller P, Varma H: A draft sequence of the rice genome (Oryza sativa L. ssp. japonica). Science 2002, 296:92-100.
24. Hirochika H, Fukuchi A, Kikuchi F: Retrotransposon families in rice. Mol Gen Genet 1992, 233:209-216.
25. Kumekawa N, Ohtsubo H, Horiuchi T, Ohtsubo E: Identification and characterisation of novel retrotransposons of the gypsy type in rice. Mol Gen Genet 1999, 260:593-602.
26. Motohashi R, Mochizuiki K, Ohtsubo H, Ohtsubo E: Structures and distribution of p-SINE1 members in rice genomes. Theor Appl Genet 1997, 95:359-68.
27. Wang SP, Liu N, Peng KM, Zhang QF: The distribution and copy number of copia-like retrotransposons in rice (Oryza sativa) and their implications in the organization and evolution of the rice genome. Proc Natl Acad Sci USA 1999, 96:6824-6828.
28. 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 colinearity with maize chromosome 4. Plant Cell 2000, 12:381-391.
29. Turcotte K, Srinivasan S, Bureau T: Survey of transposable elements from rice genomic sequences. Plant J 2001, 25:169-179.
30. Mao L, Wood TC, Yu Y, Budiman MA, Tomkins J, Woo S, Sasinowski M, Presting G, Frisch D, Goff S: Rice transposable elements: a survey of 73,000 sequence-tagged-connectors. Genome Res 2000, 10:982-990.
31. Vicient CM, Schulman AH: Copia-Like retrotransposons in the rice genome:few and assorted. Genome Letters 2002, 1:35-47.
32. McCarthy EM, Liu JD, GAO LZ, McDonald JF: LTR retrotransposons of Oryza sativa. Genome Biology 2002, 3:research0053.1-0053.11.
33. Bowen NJ, McDonald JF: Genomic analysis of Caenorhabditis elegans reveals ancient families of retroviral-like elements. Genome Res 1999, 9:924-935.
34. Ganko EW, Fielman KT, McDonald JF: Evolutionary history of Cer elements and their impact on the C. elegans Genome. Genome Res 2001, 11:2066-2074.
35. Coffin JM, Hughes SH, Varmus HE: Retroviruses New York: Cold Spring Harbor Laboratory Press; 1997.
36. Xiong Y, Eickbush TH: Origin and evolution of retroelements based upon their reverse transcriptase sequences. EMBO J 1990, 9:3353-3362.
37. SanMiguel P, Gaut BS, Tikhonov A, Nakajima Y, Bennetzen JL: The paleontology of intergene retrotransposons of maize. Nature Genet 1998, 20:43-45.
38. Bowen NJ, McDonald JF: Drosophila euchromatic LTR retrotransposons are much younger than the host species in which they reside. Genome Res 2001, 11:1527-1540.
39. Jiang N, Bao Z, Temnykh S, Cheng Z, Jiang J, Wing RA, McCouch SR, Wessler SR: Dasheng: a recently amplified nonautonomous long terminal repeat element that is a major component of pericentromeric regions in rice. Genetics 2002, 161:1293-1305.
40. Gaut BS, Morton BR, Mccaig BC, Clegg MT: Substitution rate comparisons between grasses and palms: synonymous rate differences at the nuclear gene Adh parallel rate differences at the plastid gene rbcL. Proc Natl Acad Sci USA 1996, 93:10274-10279.
41. Jordan IK, McDonald JF: Evidence for the role of recombination in the regulatory evolution of Saccharomyces cerevisiae Ty elements. J Mol Evol 1998, 47: 14-20
42. Jordan IK, McDonald JF: Phylogenetic perspective reveals abundant Ty1/Ty2 hybrid elements in the Saccharomyces cerevisiae genome. Mol Biol Evol 1999, 16:419-422.
43. Tatusova TA, Madden TL: BLAST 2 Sequences, a new tool for comparing protein and nucleotide sequences. FEMS Microbiol Lett 1999, 174:247-250.
44. 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.
45. Page RD: TreeView: An application to display phylogenetic trees on personal computers. Comput Appl Biosci 1996, 12:357-358.
46. Kumar S, Tamura K, Jakobsen IB, Nei M: MEGA (Arizona State Univ., Tempe), Version 2.1 2001.
47. Li WH: Molecular Evolution Sunderland, MA: Sinauer; 1997.
48. Cheng ZK, Presting GG, Buell CR, Wing RA, Jiang JM: High resolution pachytene chromosome mapping of bacterial artificial chromosomes anchored by genetic markers reveals the centromere location and the distribution of genetic recombination along chromosome 10 of rice. Genetics 2001, 157:1749-1757.