Retrotransposon insertion polymorphisms in six rice genes and their evolutionary history

Gene

Volumn 412, Issue 1-2, 2008, Pages 50-58

  Xu, Zijun ^a   Ramakrishna, Wusirika ^a  

^a MICHIGAN TECHNOLOGICAL UNIVERSITY   (United States)

Author keywords

Evolution; Oryza; Retrotransposons; Rice genome

Indexed keywords

ARTICLE; DNA POLYMORPHISM; GENE IDENTIFICATION; GENE INSERTION; GENETIC CONSERVATION; GENOME; NUCLEOTIDE SEQUENCE; PHYLOGENY; PRIORITY JOURNAL; RETROPOSON; RICE; SHORT INTERSPERSED REPEAT; TRANSPOSON;

BASE SEQUENCE; CONSERVED SEQUENCE; DNA, PLANT; EVOLUTION, MOLECULAR; GENES, PLANT; ORYZA SATIVA; PHYLOGENY; POLYMERASE CHAIN REACTION; POLYMORPHISM, GENETIC; RETROELEMENTS; SPECIES SPECIFICITY;

EMBRYOPHYTA; ORYZA; ZIZANIA;

EID: 40649115913     PISSN: 03781119     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.gene.2008.01.012     Document Type: Article

References (51)

1. Altschul S.F., et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25 (1997) 3389-3402
2. Bautista N.S., Solis R., Kamijima O., and Ishii T. RAPD, RFLP and SSLP analyses of phylogenetic relationships between cultivated and wild species of rice. Genes Genet. Syst. 76 (2001) 71-79
3. Chang T.T. The origin, evolution, cultivation, dissemination, and diversification of Asian and African rices. Euphytica 25 (1976) 435-441
4. Chung H., et al. Cis-regulatory elements in the Accord retrotransposon result in tissue-specific expression of the Drosophila melanogaster insecticide resistance gene Cyp6g1. Genetics 175 (2007) 1071-1077
5. Daborn P.J., et al. A single P450 allele associated with insecticide resistance in Drosophila. Science 297 (2002) 2253-2256
6. Duan S., et al. Phylogenetic analysis of AA-genome Oryza species (Poaceae) based on chloroplast, mitochondrial, and nuclear DNA sequences. Biochem. Genet. 45 (2007) 113-129
7. Garris A.J., Tai T.H., Coburn J., Kresovich S., and McCouch S. Genetic structure and diversity in Oryza sativa L. Genetics 169 (2005) 1631-1638
8. Ge S., Sang T., Lu B., and Hong D. Phylogeny of rice genomes with emphasis on origins of allotetraploid species. Proc. Natl. Acad. Sci. U. S. A. 96 (1999) 14400-14405
9. International Rice Genome Sequencing Project. The map-based sequence of the rice genome. Nature 436 (2005) 793-800
10. Jiao Y., and Deng X.W. A genome-wide transcriptional activity survey of rice transposable element-related genes. Genome Biol. 8 (2007) R28
11. Jurka J. Repbase update: a database and an electronic journal of repetitive elements. Trends Genet. 9 (2000) 418-420
12. Kader J.-C. Lipid-transfer proteins in plants. Annu. Rev. Plant Physiol. Plant Mol. Biol. 47 (1996) 627-654
13. Kawase M., Fukunaga K., and Kato K. Diverse origins of waxy foxtail millet crops in East and Southeast Asia mediated by multiple transposable element insertions. Mol. Genet. Genomics 274 (2005) 131-140
14. Khush G.S. Origin, dispersal, cultivation and variation of rice. Plant Mol. Biol. 35 (1997) 25-34
15. Kikuchi S., et al. Collection, mapping, and annotation of 28,000 full-length cDNA clones from Japonica rice. Science 301 (2003) 376-379
16. Kobayashi S., Yamamoto N., and Hirochika H. Retrotransposon-induced mutations in grape skin color. Science 304 (2004) 982
17. Krom, N., Recla, J., Ramakrishna, W., in press. Analysis of genes associated with retrotransposons in the rice genome. Genetica. doi.10.1007/s10709-007-9237-3.
18. Kumar A., and Bennetzen J.L. Plant retrotransposons. Annu. Rev. Genet. 33 (1999) 479-532
19. Kumar S., Tamura K., and Nei M. MEGA3: integrated software for molecular evolutionary genetics analysis and sequence alignment. Brief. Bioinform. 5 (2004) 150-163
20. Lerman D.N., and Feder M.E. Naturally occurring transposable elements disrupt hsp70 promoter function in Drosophila melanogaster. Mol. Biol. Evol. 22 (2005) 776-783
21. Lerman D.N., Michalak P., Helin A.B., Bettencourt B.R., and Feder M.E.P. Modification of heat-shock gene expression in Drosophila melanogaster populations via transposable elements. Mol. Biol. Evol. 20 (2003) 135-144
22. Londo J.P., Chiang Y.C., Hung K.H., Chiang T.Y., and Schaal B.A. Phylogeography of Asian wild rice, Oryza rufipogon, reveals multiple independent domestications of cultivated rice, Oryza sativa. Proc. Natl. Acad. Sci. U. S. A. 103 (2006) 9579-9583
23. Ma J., and Bennetzen J.L. Rapid recent growth and divergence of rice nuclear genomes. Proc. Natl. Acad. Sci. U. S. A. 101 (2004) 12404-12410
24. Mochizuki K., Ohtsubo H., Hirano H., Sano Y., and Ohtsubo E. Classification and relationships of rice strains with AA genome by identification of transposable elements at nine loci. Jpn. J. Genet. 68 (1993) 205-217
25. Nishikawa T., Vaughan D.A., and Kadowaki K. Phylogenetic analysis of Oryza species, based on simple sequence repeats and their flanking nucleotide sequences from the mitochondrial and chloroplast genomes. Theor. Appl. Genet. 110 (2005) 696-705
26. Nobuta K., et al. An expression atlas of rice mRNAs and small RNAs. Nat. Biotechnol. 25 (2007) 473-477
27. Nouaud D., and Anxolabehere D. P element domestication: a stationary truncated P element may encode a 66-kDa repressor-like protein in the Drosophila montium species subgroup. Mol. Biol. Evol. 14 (1997) 1132-1144
28. Nouaud D., Boeda B., Levy L., and Anxolabehere D. A P element has induced intron formation in Drosophila. Mol. Biol. Evol. 16 (1999) 1503-1510
29. Nouaud D., Questneville H., and Anxolabehere D. Recurrent exon shuffling between distant P-element families. Mol. Biol. Evol. 20 (2003) 190-199
30. Oka H.I. Origin of Cultivated Rice (1988), Elsevier, Tokyo
31. Piegu B., et al. Doubling genome size without polyploidization: dynamics of retrotransposition-driven genomic expansions in Oryza australiensis, a wild relative of rice. Genome Res. 16 (2006) 1262-1269
32. Prathepha P., and Samappito S. Use of the p-SINE1-r2 in inferring evolutionary relationships of Thai rice varieties with AA genome. Songklanakarin J. Sci. Technol. 28 (2006) 39-48
33. Ramakishana W., Lagu M.D., Gupta V.S., and Ranjekar P.K. DNA fingerprinting in rice with oligonucleotide probes specific for simple repetitive DNA sequences. Theor. Appl. Genet. 88 (1994) 402-406
34. Ramakrishna W., et al. Different types and rates of genome evolution detected by comparative sequence analysis of orthologous segments from four cereal genomes. Genetics 162 (2002) 1389-1400
35. Reiss D., Nouaud D., Ronsseray S., and Anxolabehere D. Domesticated P elements in the Drosophila montium species subgroup have a new function related to a DNA binding property. J. Mol. Evol. 61 (2005) 470-480
36. m. Funct. Integr. Genomics 2 (2002) 70-80
37. Schlenke T.A., and Begun D.J. Strong selective sweep associated with a transposon insertion in Drosophila simulans. Proc. Natl. Acad. Sci. U. S. A. 101 (2004) 1626-1631
38. Schulman A.H., Flavell A.J., and Ellis T.H. The application of LTR retrotransposons as molecular markers in plants. Methods Mol. Biol. 260 (2004) 145-173
39. Sharma S.D. Evolutionary trends in the genus Oryza. Rice Genet (1986), IRRI, Los Banos, Phillipines 59-67
40. Song W.-Y., Pi L.Y., Wang G.L., Gardner J., Holsten T., and Ronald P.C. Evolution of the rice Xa21 disease resistance gene family. Plant Cell 9 (1997) 1279-1287
41. Sweeney M., and McCouch S. The complex history of the domestication of rice. Annals Botany (2007) 1-7
42. Vaughan D.A., Kadowaki K., Kaga A., and Tomooka N. On the phylogeny and biogeography of the genus Oryza. Breed. Sci. 55 (2005) 113-122
43. Vitte C., Panaud O., and Quesneville H. LTR retrotransposons in rice (Oryza sativa, L.): recent burst amplifications followed by rapid DNA loss. BMC Genomics 8 (2007) 218
44. Walker A.R., Lee E., Bogs J., McDavid D.A.J., Thomas M.R., and Robinson S.P. White grapes arose through the mutation of two similar and adjacent regulatory genes. Plant J. 49 (2007) 772-785
45. Walser J.C., Chen B., and Feder M.E. Heat-shock promoters: targets for evolution by P transposable elements in Drosophila. PLOS Genet. 2 (2006) 1541-1555
46. Wang Z.X., et al. The Pib gene for rice blast resistance belongs to the nucleotide binding and leucine-rich repeat class of plant disease resistance genes. Plant J. 19 (1999) 55-64
47. Wang G.L., et al. Isolation and characterization of rice mutants compromised in Xa21-mediated resistance to X. oryzae pv. oryzae. Theor. Appl. Genet. 108 (2004) 379-384
48. Wicker T., et al. A unified classification system for eukaryotic transposable elements. Nat. Rev. 8 (2007) 973-982
49. Witte C.-P., Le Q.H., Bureau T., and Kumar A. Terminal-repeat retrotransposons in miniature (TRIM) are involved in restructuring plant genomes. Proc. Natl. Acad. Sci. U. S. A. 98 (2001) 13778-13783
50. Xu J.H., Cheng C., Tsuchimoto S., Ohtsubo H., and Ohtsubo E. Phylogenetic analysis of Oryza rufipogon strains and their relations to Oryza sativa strains by insertion polymorphism of rice SINEs. Genes Genet. Syst. 82 (2007) 217-229
51. Yu J., et al. A draft sequence of the rice genome (Oryza sativa L. ssp indica). Science 296 (2002) 79-92