Quantification of the retrotransposon BARE-1 reveals the dynamic nature of the barley genome

Genome

Volumn 49, Issue 4, 2006, Pages 389-396

  Soleimani, V D ^a   Baum, B R ^a   Johnson, D A ^b  

^a AGRICULTURE AND AGRI FOOD CANADA   (Canada)

^b UNIVERSITY OF OTTAWA   (Canada)

Author keywords

BARE 1; Genome evolution; Quantification; Real time PCR; Retrotransposons

Indexed keywords

BARE 1 PROTEIN, HORDEUM VULGARE; BARE-1 PROTEIN, HORDEUM VULGARE; RNA DIRECTED DNA POLYMERASE; VEGETABLE PROTEIN;

ARTICLE; BARLEY; BREEDING; COMPARATIVE STUDY; GENE DOSAGE; GENETIC SELECTION; GENETICS; GENOME; METHODOLOGY; MOLECULAR CLONING; POLYMERASE CHAIN REACTION; RETROPOSON; SPECIES DIFFERENCE; STANDARD;

BREEDING; CLONING, MOLECULAR; GENE DOSAGE; GENOME, PLANT; HORDEUM; PLANT PROTEINS; POLYMERASE CHAIN REACTION; RETROELEMENTS; RNA-DIRECTED DNA POLYMERASE; SELECTION (GENETICS); SPECIES SPECIFICITY;

HORDEUM VULGARE; HORDEUM VULGARE SUBSP. SPONTANEUM; HORDEUM VULGARE SUBSP. VULGARE;

EID: 33745873501     PISSN: 08312796     EISSN: None     Source Type: Journal    
DOI: 10.1139/G05-119     Document Type: Article

References (46)

1. Altschul, S.F., Gish, W., Miller, W., Myers, E.W., and Lipman, D.J. 1990. Basic local alignment search tool. J. Mol. Biol. 215: 403-410.
2. Bennetzen, J.L., and Kellogg, E.A. 1997. Do plants have a one-way ticket to genome obesity? Plant Cell, 9: 1509-1514.
3. Devos, K.M., Brown, J.K.M., and Bennetzen, J.L. 2002. Genome size reduction through illegitimate recombination counteracts genome expansion in Arabidopsis. Genome Res. 12: 1075-1079.
4. Flavell, A.J., Dunbar, E., Anderson, R., Pearce, S.R., Hartley, R., and Kumar, A. 1992. Ty1-copia group retrotransposons are ubiquitous and heterogeneous in higher plants. Nucleic Acids Res. 20: 3639-3644.
5. Gibson, U.E., Heid, C.A., and Williams, P.M. 1996. A novel method for real time quantitative RT-PCR. Genome Res. 6: 995-1001.
6. Grandbastien, M.A., Lucas, H., Morel, J.B., Mhiri, C., Vernhettes, S., and Casacuberta, J.M. 1997. The expression of the tobacco Tnt1 retrotransposon is linked to plant defense response. Genetica, 100: 241-252.
7. Gu, Y.Q., Anderson, O.D., Londeore, C.F., Kong, X., Chbbar, R.N., and Lazo, G.R. 2003. Structural organization of the barley D-hordein locus in comparison with its orthologous region in wheat genomes. Genome, 46: 1084-1097.
8. Heid, C.A., Stevens, A.J., Livak, K.J., and Williams, P.M. 1996. Real-time quantitative PCR. Genome Res. 6: 986-994.
9. Higuchi, R., Dollinger, G., Walsh, P.S., and Grifith, R. 1992. Simultaneous amplification and detection of specific DNA sequences. Bio/Technology, 10: 413-417.
10. Hirochika, H. 1993. Activation of tobacco retrotransposons during tissue culture. EMBO J. 12: 2521-2528.
11. Hirochika, H., Sugimoto, K., Otsuki, Y., and Kanda, M. 1996. Retrotransposons of rice involved in mutations induced by tissue culture. Proc. Natl. Acad. Sci. U.S.A. 93: 7783-7788.
12. Horsely, R.D., Schwarz, P.B., and Hammond, J.J. 1995. Genetic diversity in malt quality of North American six-rowed spring barley. Crop. Sci. 35: 113-118.
13. Jaaskelainen, M., Mykkanen, A.H., Arna, T., Vicient, C., Suoniemi, A., Kalendar, A., Savilahti, H., and Schulman, A.H. 1999. Retrotransposon BARE-1: expression of encoded proteins and formation of virus-like particles in barley cells. Plant J. 20: 413-422.
14. Kaeppler, S.M., Kaeppler, H.F., and Rhee, Y. 2000. Epigenetic aspects of somaclonal variation. Plant Mol. Biol. 43: 179-188.
15. Kalendar, R. 2001. Oligos©. A computer program for the design of PCR primers. Institute of Biotechnology, University of Helsinki, Finland. Available from http://www.biocenter.helsinki.fi/bi/bare-1_html/download.htm.
16. Kalendar, R., Tanskanen, J., Immonen, S., Nevo, E., and Schulman, A. 2000. Genome evolution of wild barley (Hordeum spontaneum) by BARE-1 retrotransposon dynamics in response to sharp microclimatic divergence. Proc. Natl. Acad. Sci. U.S.A. 97: 6603-6607.
17. Kalendar, R., Vicient, C.M., Peleg, O., Anamthawat-Jonsson, K., Bolshoy, A., Schulman, A.H. 2004. Large retrotransposon derivatives: abundance, conserved but non-autonomous retroelements of barley and related genomes. Genetics, 166: 1437-1450.
18. Kashkush, K., Feldman, M., and Levy, A.A. 2003. Transcriptional activation of retrotransposons alters the expression of adjacent genes in wheat. Nat. Genet. 33: 102-106.
19. Kshirsagar, A.M. 1972. Multivariate analysis. Marcel Dekker, New York, N.Y.
20. Kubis, S.E., Castilho, M.M.F., Vershinin, A.V., and Heslop-Harrison, J.S. 2003. Retroelements, transposons and methylation status in the genome of oil palm (Elaeis guineensis) and the relationship to somaclonal variation. Plant Mol. Biol. 52: 69-79.
21. Kumar, A., and Bennetzen, J.L. 1999. Plant retrotransposons. Annu. Rev. Genet. 33: 479-532.
22. Liu, B., and Wendel, J.F. 2000. Retrotransposon activation followed by rapid repression in introgressed rice plants. Genome, 43: 874-880
23. Ma, J., Devos, K.M., and Bennetzen, J.L. 2004. Analyses of LTR-retrotransposon structures reveal recent and rapid genomic DNA loss in rice. Genome Res. 14: 860-869.
24. Manninen, I., and Schulman, A.H. 1993. BARE-1, a copia-like retroelement in barley (Hordeum vulgare L). Plant Mol. Biol. 22: 829-846.
25. Martin, J.M., Blake, T.K., and Hockett, E.A. 1991. Diversity among North American spring barley based on coefficient of parentage. Crop Sci. 31: 1131-1137.
26. Michaud, E.J., van Vugt, M.J., Bultman, S.J., Sweet, O.H., Davidson, M.T., and Woychik, R.P. 1994. Differential expression of a new dominant agouti allele (Aiapy) is correlated with methylation state and is influenced by parental lineage. Genes Dev. 8: 1463-1472.
27. Panstruga, R., Buschges, R., Piffanelli, P., and Schultz-Lefert, P. 1998. A contiguous 60 kb genomic stretch from barley reveals molecular evidence for gene islands in a monocot genome. Nucleic Acids Res. 26: 1056-1062.
28. Pearce, S.R., Kumar, A., and Flavell, A.J. 1996a. Activation of the Ty1-copia group retrotransposons of potato (Solanum tuberosum) during protoplast isolation. Plant Cell Rep. 15: 949-953.
29. Pearce, S.R., Harrison, G., Li, D., Heslop-Harrison, J.S., Kumar, A., and Flavell, A.J. 1996b. The Ty1-copia group retrotransposons in Vicia species: copy number, sequence heterogeneity and chromosomal localization. Mol. Gen. Genet. 250: 305-315.
30. Pereira, V. 2004. Insertion bias and purifying selection for retrotransposons in the Arabidopsis thaliana genome. Genome Biol. 5: R79.
31. Poteau, S., Huttner, E., Grandbastien, M.A., and Caboche, M. 1991. Specific expression of the tobacco Tnt1 retrotransposon in protoplast. EMBO J. 10: 1911-1918.
32. Rao, C.R. 1952. Advanced statistical methods in biometric research. Wiley, New York, N.Y.
33. Sanger, F., Nicklen, S., and Coulson, A.R. 1997. DNA sequencing with chain terminating inhibitors. Proc. Natl. Acad. Sci. U.S.A. 74: 5463-5467.
34. SanMiguel, P., Tikhonov, A., Jin, Y.K., Motchoulskaia, N., Zakharov, D., Melake-Berhan, A., Springer, P.S., Edwards, K.J., Lee, M., Avramova, Z., and Bennetzen, J.L. 1996. Nested retrotransposons in the intergenic regions of the maize genome. Science (Washington, D.C.), 274: 765-767.
35. SanMiguel, P., Gaut, B.S., Tikhonov, A., Nakajima, Y., and Bennetzen, J.L. 1998. The palaeontology of integrase retrotransposons of maize. Nat. Genet. 20: 43-45.
36. SAS Institute Inc. 2002. SAS/STAT® user's guide, version 9.1. SAS Institute Inc., Cary, N.C.
37. Shirasu, K., Schulman, A.H., Lahaye, T., and Schulze-Lefert, P. 2000. A contiguous 66-kb barley DNA sequence provides evidence for reversible genome expansion. Genome Res. 10: 908-915.
38. Suoniemi, A., Schmidt, D., and Schulman, A.H. 1996a. The BARE-1 retrotransposon is transcribed in barley from an LTR promoter active in transient assay. Plant Mol. Biol. 31: 295-306.
39. Suoniemi, A., Anamthawat-Jonsson, K., Arna, T., and Schulman, A.H. 1996b. Retrotransposon BARE-1 is a major, dispersed component of barley (Hordeum vulgare L.) genome. Plant Mol. Biol. 30: 1321-1329.
40. Takeda, S., Sugimoto, K., Otsuki, H., and Hirochika, H. 1998. Transcriptional activation of the tobacco retrotransposon Tto1 by wounding and methyl jasmonate. Plant Mol. Biol. 36: 365-376.
41. Vernhettes, S., Grandbastien, M.-A., and Casacuberta, J.M. 1997. In vivo characterization of transcriptional regulatory sequences involved in the defence-associated expression of the tobacco Tnt1. Plant Mol. Biol. 35: 673-679.
42. Vershinin, A.V., Salina, E.A., Solovyov, V.V., and Timofeyeva, L.L. 1990. Genomic organization, evolution and structural peculiarities of high repetitive DNA of Hordeum vulgare. Genome, 33: 441-449.
43. Vicient, C.M., Sioniemi, A., Anamthawat-Jonsson, K., Tanslanen, J., Beharav, A., Nevo, E., and Schulman, A.H. 1999. Retrotransposon BARE-1 and its role in genome evolution in the genus Hordeum. The Plant Cell, 11: 1769-1784.
44. Waugh, R., Mclean, K., Flavell, A.J., Pearce, S.R., and Kumar, A. 1997. Genetic distribution of BARE-1-like retrotransposable elements in the barley genome revealed by sequence-specific amplified polymorphism (S-SAP). Mol. Gen. Genet. 253: 687-694.
45. Wicker, T., Stein, N., Albar, L., Feuillet, C., Schlagenhauf, E., and Keller, B. 2001. Analysis of a contiguous 211 kb sequence in diploid wheat (Triticum monococcum L.) reveals multiple mechanisms of genome evolution. Plant J. 26: 307-316.
46. Zhang, X., and Wessler, S.R. 2004. Genome-wide comparative analysis of the transposable elements in related species Arabidopsis thaliana and Brassica oleracea. Proc. Natl. Acad. Sci. U.S.A. 101: 5589-5594.