Acknowledgements


We would like to thank Drs. Phillip John SanMiguel (Director of the Genomics Core Facility, Purdue University), Jeff Bennetzen (Purdue University) and Jo Messing (Rutgers University), for donating unpublished maize transposable element sequences to the Gramineae Repeat Database and Zea Repeat Database.

Funding for this work was provided by a grant to C. Robin Buell from the U. S. Department of Agriculture (99-35317-8275), the National Science Foundation (DBI-998282), and the U. S. Department of Energy (DE-FG02-99ER20357; DE-FG02-01ER15265).




Selected references


Cheng Z., Dong F., Langdon T., Ouyang S., Buell C.R., Gu M., Blattner F.R. and Jiang J. (2002) Functional rice centromeres are marked by a satellite repeat and a centromere-specific retrotransposon. Plant Cell 14:1691-1704

Jiang, N. and Wessler, S.R. (2001) Insertion Preference of Maize and Rice Miniature Inversted Repeat Transposable Elements as Revealed by the Analysis of Nested Elements. Plant Cell 13:2553-2564

Temnykh, S., DeClerck, G., Lukashova, A., Lipovich, L., Cartinhour, S. and McCouch S. (2001) Computational and Experimental Analysis of Microsatellites in Rice (Oryza sativa L.): Frequency, Length Variation, Transposon Assocaitions, and Genetic Marker Potenital. Genome Res. 11:1441-1452

Turcotte, K., Srinivasan S. and Bureau, T. (2001) Surey of Transposable Elements from Rice Genomic Sequences. Plant J. 25:169-179

Zhang Q., Arbuckle J. and Wessler S.R. (2000)Recent, extensive, and preferential insertion of members of the miniature inverted-repeat transposable element family Heartbreaker into genic regions of maize. Proc. Natl. Acad. Sci. U S A 97:1160-1165

Mao, L., Wood, T.C., Yu, Y., Budiman, M.A., Tomkins, J., Woo, S., Sasinowski, M., Presting, G., Frisch, D. Goff, S., Dean, R.A. and Wing, R.A. (2000) Rice Transposable Elements: A Survey of 73,000 Sequence-Tagged-Connectors. Genome Res. 10:982-990

Tarchini, R., Biddle, P., Wineland, R., Tingey, S. and 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

Schmidt T. (1999) LINEs, SINEs and repetitive DNA: non-LTR retrotransposons in plant genomes. Plant Mol. Biol. 40:903-10

Dong, F., Miller, J.T., Jackson, S.A., Wang, G-L., Ronald, P.C. and Jiang, J. (1998) Rice (Orzya sativa) centromeric regions consist of complex DNA. Proc. Natl. Acad. Sci. 95:8135-8140

Song, W.-Y., Pi, L.-Y., Bureau. T.E. and Ronald, P.C. (1998) Identification and characterization of 14 transposon-like elements in the noncoding regions of members of the Xa21 family of disease resistance genes in rice. Mol. Gen. Genet. 258:449-456

Yoshida, S., Tamaka, K., Watanabe, K., Fujino, M. and Nakamura, C. (1998) A maize MuDR-like element expressed in rice callus subcultured with proline. Hereditas 129:95-99

Hirochika, H. (1997) Retrotransposons of rice: their regulation and use for genome analysis. Plant Molecular Biology 35:231-240

McCouch, S.R., Chen, X., Panaud, O., Temnykh, X., Zu, Y, Cho, Y.G., Huang, N., Ishii, T. and Blair, M. (1997) Microsatellite marker development, mapping and applications in rice genetics and breeding. Plant Molecular Biology 35:89-99

Ohmido, N. and Fukui, K. (1997) Visual verification of close disposition between a rice genomic-specific DNA sequence (TrsA) and the telomere sequence. Plant Molecular Biology 35:963-968

Bureau, T.E., Ronald, P.C. and Wessler, S.R. (1996) A computer based systemic survey reveals the predominance of small inverted-repeat elements in wild-type rice genes. Proc. Natl. Acad. Sci. 93:8524-8529

Motohashi, R., Ohtsubo, E. and Ohtsubo, H. (1996) Identification of Tnr3, a suppressor-mutator/enhancer-like transposable element from rice. Mol. Gen. Genet. 250:148-152

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 274:765-768

Fukui, K., Ohmido, N. and Khush, G.S. (1994) Variability in rDNA loci in genus Oryza detected through fluorescence in situ hybridization. Theor. Appl. Genet. 87:893-899

Wu, T., Wang, Y. and Wu, R. (1994) Transcribed repetitive DNA sequences in telomeric regions of rice. Plant Molecular Biology 26:363-375

Arumuganathan, K. and Earle, E.D. (1991) Nuclear DNA content of some important plant species. Plant Molecular Biology Reporter 9:208-218

McCouch, S.R., Kochert, G., Z..H., Y., Wang, Z.Y., Khush, G.S., Coffman, W.R. and Tanksley, S.D. (1988) Molecular mapping of rice chromosomes. Theor Appl Genet, 76, 815-829

Flavell, R.B., Bennett, M.D., Smith, J.B. and Smith, D.B. (1974) Genome size and the proportion of repeated nucleotide sequence DNA in plants. Biochem Genet. 12:257-269