Gene duplication and exon shuffling by helitron-like transposons generate intraspecies diversity in maize

Kapitonov, V.V. & Jurka, J. Rolling-circle transposons in eukaryotes. Proc. Natl. Acad. Sci. USA 98, 8714–8719 (2001).

Poulter, R.T., Goodwin, T.J. & Butler, M.I. Vertebrate helentrons and other novel Helitrons . Gene 313, 201–212 (2003).

Lal, S.K., Giroux, M.J., Brendel, V., Vallejos, C.E. & Hannah, L.C. The maize genome contains a helitron insertion. Plant Cell 15, 381–391 (2003).

Fu, H. & Dooner, H.K. Intraspecific violation of genetic colinearity and its implications in maize. Proc. Natl. Acad. Sci. USA 99, 9573–9578 (2002).

Song, R. & Messing, J. Gene expression of a gene family in maize based on noncollinear haplotypes. Proc. Natl. Acad. Sci. USA 100, 9055–9060 (2003).

Brunner, S., Fengler, K., Morgante, M., Tingey, S. & Rafalski, A. Evolution of DNA sequence nonhomologies among maize inbreds. Plant Cell 17, 343–360 (2005).

Meyers, B.C., Scalabrin, S. & Morgante, M. Mapping and sequencing complex genomes: let's get physical! Nat. Rev. Genet. 5, 578–588 (2004).

Gardiner, J. et al. Anchoring 9,371 maize expressed sequence tagged unigenes to the bacterial artificial chromosome contig map by two-dimensional overgo hybridization. Plant Physiol. 134, 1317–1326 (2004).

Bennetzen, J.L., Coleman, C., Liu, R., Ma, J. & Ramakrishna, W. Consistent over-estimation of gene number in complex plant genomes. Curr. Opin. Plant Biol. 7, 732–736 (2004).

Palmer, L.E. et al. Maize genome sequencing by methylation filtration. Science 302, 2115–2117 (2003).

Messing, J. et al. Sequence composition and genome organization of maize. Proc. Natl Acad. Sci. USA 101, 14349–14354 (2004).

Ramakrishna, W., Emberton, J., Ogden, M., SanMiguel, P. & Bennetzen, J.L. Structural analysis of the maize rp1 complex reveals numerous sites and unexpected mechanisms of local rearrangement. Plant Cell 14, 3213–3223 (2002).

Craig, N.L., Craigie, R., Gellert, M. & Lambowitz, A.M. Mobile DNA II (American Society of Microbiology Press, Washington, DC, 2002).

Gupta, S., Gallavotti, A., Stryker, G.A., Schmidt, R.J. & Lal, S.K. A novel class of Helitron-related transposable elements in maize contains portions of multiple pseudogenes. Plant Mol. Biol. 57, 115–127 (2005).

Feschotte, C. & Wessler, S.R. Treasures in the attic: rolling circle transposons discovered in eukaryotic genomes. Proc. Natl. Acad. Sci. USA 98, 8923–8924 (2001).

Kynast, R.G. et al. A complete set of maize individual chromosome additions to the oat genome. Plant Physiol. 125, 1216–1227 (2001).

Okagaki, R.J. et al. Mapping maize sequences to chromosomes using oat-maize chromosome addition materials. Plant Physiol. 125, 1228–1235 (2001).

Song, R., Llaca, V. & Messing, J. Mosaic organization of orthologous sequences in grass genomes. Genome Res. 12, 1549–1555 (2002).

Lai, J. et al. Gene loss and movement in the maize genome. Genome Res. 14, 1924–1931 (2004).

Swigonova, Z., Bennetzen, J.L. & Messing, J. Structure and evolution of the r/b chromosomal regions in rice, maize, and sorghum. Genetics 169, 891–906 (2005).

Ilic, K., SanMiguel, P.J. & Bennetzen, J.L. A complex history of rearrangement in an orthologous region of the maize, sorghum, and rice genomes. Proc. Natl. Acad. Sci. USA 100, 12265–12270 (2003).

Hamilton, A.J. & Baulcombe, D.C. A species of small antisense RNA in posttranscriptional gene silencing in plants. Science 286, 950–952 (1999).

van der Krol, A.R., Mur, L.A., Beld, M., Mol, J.N. & Stuitje, A.R. Flavonoid genes in petunia: addition of a limited number of gene copies may lead to a suppression of gene expression. Plant Cell 2, 291–299 (1990).

Duvick, D.N. Biotechnology in the 1930s: the development of hybrid maize. Nat. Rev. Genet. 2, 69–74 (2001).

Birchler, J.A., Auger, D.L. & Riddle, N.C. In search of the molecular basis of heterosis. Plant Cell 15, 2236–2239 (2003).

Jiang, N., Bao, Z., Zhang, X., Eddy, S.R. & Wessler, S.R. Pack-MULE transposable elements mediate gene evolution in plants. Nature 431, 569–573 (2004).

Yu, Z., Wright, S.I. & Bureau, T.E. Mutator-like elements in Arabidopsis thaliana. Structure, diversity and evolution. Genetics 156, 2019–2031 (2000).

Le, Q.H., Wright, S., Yu, Z. & Bureau, T. Transposon diversity in Arabidopsis thaliana . Proc. Natl. Acad. Sci. USA 97, 7376–7381 (2000).

Lai, J., Li, Y., Messing, J. & Dooner, H.K. Gene movement by Helitron transposons contributes to the haplotype variability of maize. Proc. Natl. Acad. Sci. USA 102, 9068–9073 (2005).

Meyers, B.C., Tingey, S.V. & Morgante, M. Abundance, distribution, and transcriptional activity of repetitive elements in the maize genome. Genome Res. 11, 1660–1676 (2001).