How important are transposons for plant evolution? (original) (raw)

• Bennetzen, J. L., Ma, J. & Devos, K. M. Mechanisms of recent genome size variation in flowering plants. Ann. Bot. 95, 127–132 (2005).
  Article CAS PubMed PubMed Central Google Scholar
• Dooner, H. K. & Weil, C. F. Give-and-take: interactions between DNA transposons and their host plant genomes. Curr. Opin. Genet. Dev. 17, 486–492 (2007).
  Article CAS PubMed Google Scholar
• Feschotte, C. Transposable elements and the evolution of regulatory networks. Nature Rev. Genet. 9, 397–405 (2008).
  Article CAS PubMed Google Scholar
• Tollis, M. & Boissinot, S. The evolutionary dynamics of transposable elements in eukaryote genomes. Genome Dyn. 7, 68–91 (2012).
  Article CAS PubMed Google Scholar
• Candela, H. & Hake, S. The art and design of genetic screens: maize. Nature Rev. Genet. 9, 192–203 (2008).
  Article CAS PubMed Google Scholar
• Hsing, Y. et al. A rice gene activation/knockout mutant resource for high throughput functional genomics. Plant Mol. Biol. 63, 351–364 (2007).
  Article CAS PubMed Google Scholar
• Settles, A. M. et al. Sequence-indexed mutations in maize using the UniformMu transposon-tagging population. BMC Genomics 8, 116 (2007).
  Article PubMed PubMed Central CAS Google Scholar
• Singer, T., Yordan, C. & Martienssen, R. A. Robertson's mutator transposons in A. thaliana are regulated by the chromatin-remodeling gene decrease in DNA methylation (DDM1). Genes Dev. 15, 591–602 (2001).
  Article CAS PubMed PubMed Central Google Scholar
• Tsukahara, S. et al. Bursts of retrotransposition reproduced in Arabidopsis. Nature 461, 423–426 (2009).
  Article CAS PubMed Google Scholar
• Wang, H. Y. et al. Transpositional reactivation of two LTR retrotransposons in rice-Zizania recombinant inbred lines (RILs). Hereditas 147, 264–277 (2010).
  Article PubMed Google Scholar
• McClintock, B. The significance of responses of the genome to challenge. Science 226, 792–801 (1984).
  Article CAS PubMed Google Scholar
• Lin, C. et al. Dramatic genotypic difference in, and effect of genetic crossing on, tissue culture-induced mobility of retrotransposon Tos17 in rice. Plant Cell Rep. 31, 2057–2063 (2012).
  Article CAS PubMed Google Scholar
• Naito, K. et al. Dramatic amplification of a rice transposable element during recent domestication. Proc. Natl Acad. Sci. USA 103, 17620–17625 (2006).
  Article CAS PubMed PubMed Central Google Scholar
• Ungerer, M. C., Strakosh, S. C. & Zhen, Y. Genome expansion in three hybrid sunflower species is associated with retrotransposon proliferation. Curr. Biol. 16, R872–873 (2006).
  Article CAS PubMed Google Scholar
• Kalendar, R., Tanskanen, J., Immonen, S., Nevo, E. & Schulman, A. H. Genome evolution of wild barley (Hordeum spontaneum) by BARE-1 retrotransposon dynamics in response to sharp microclimatic divergence. Proc. Natl Acad. Sci. USA 97, 6603–6607 (2000).
  Article CAS PubMed PubMed Central Google Scholar
• Wessler, S. R. Turned on by stress. Plant retrotransposons. Curr. Biol. 6, 959–961 (1996).
  Article CAS PubMed Google Scholar
• Maumus, F. et al. Potential impact of stress activated retrotransposons on genome evolution in a marine diatom. BMC Genomics 10, 624 (2009).
  Article PubMed PubMed Central CAS Google Scholar
• Kawase, M., Fukunaga, K. & Kato, K. Diverse origins of waxy foxtail millet crops in East and Southeast Asia mediated by multiple transposable element insertions. Mol. Genet. Genom. 274, 131–140 (2005). This comprehensive analysis of hundreds of accessions of foxtail millet demonstrates that all known 'sticky' accessions in this species are the result of TE-induced mutations of the waxy locus.
  Article CAS Google Scholar
• Bhattacharyya, M. K., Smith, A. M., Ellis, T. H., Hedley, C. & Martin, C. The wrinkled-seed character of pea described by Mendel is caused by a transposon-like insertion in a gene encoding starch-branching enzyme. Cell 60, 115–122 (1990).
  Article CAS PubMed Google Scholar
• Kobayashi, S., Goto-Yamamoto, N. & Hirochika, H. Retrotransposon-induced mutations in grape skin color. Science 304, 982 (2004).
  Article PubMed Google Scholar
• Cadle-Davidson, M. M. & Owens, C. L. Genomic amplification of the Gret1 retroelement in white-fruited accessions of wild vitis and interspecific hybrids. Theor. Appl. Genet. 116, 1079–1094 (2008).
  Article CAS PubMed Google Scholar
• Shimazaki, M., Fujita, K., Kobayashi, H. & Suzuki, S. Pink-colored grape berry is the result of short insertion in intron of color regulatory gene. PLoS ONE 6, e21308 (2011).
  Article CAS PubMed PubMed Central Google Scholar
• Yao, J., Dong, Y. & Morris, B. A. Parthenocarpic apple fruit production conferred by transposon insertion mutations in a MADS-box transcription factor. Proc. Natl Acad. Sci. USA 98, 1306–1311 (2001).
  Article CAS PubMed PubMed Central Google Scholar
• Clegg, M. T. & Durbin, M. L. Tracing floral adaptations from ecology to molecules. Nature Rev. Genet. 4, 206–215 (2003).
  Article CAS PubMed Google Scholar
• Clegg, M. T. & Durbin, M. L. Flower color variation: a model for the experimental study of evolution. Proc. Natl Acad. Sci. USA 97, 7016–7023 (2000).
  Article CAS PubMed PubMed Central Google Scholar
• Park, K. I. et al. A bHLH regulatory gene in the common morning glory, Ipomoea purpurea, controls anthocyanin biosynthesis in flowers, proanthocyanidin and phytomelanin pigmentation in seeds, and seed trichome formation. Plant J. 49, 641–654 (2007).
  Article CAS PubMed Google Scholar
• Glover, D., Durbin, M., Huttley, G. & Clegg, M. T. Genetic diversity in the common morning glory. Plant Species Biol. 11, 41–50 (1996).
  Article Google Scholar
• Doebley, J. F., Gaut, B. S. & Smith, B. D. The molecular genetics of crop domestication. Cell 127, 1309–1321 (2006).
  Article CAS PubMed Google Scholar
• Pelsy, F. Molecular and cellular mechanisms of diversity within grapevine varieties. Heredity 104, 331–340 (2010).
  Article CAS PubMed Google Scholar
• Izawa, T., Konishi, S., Shomura, A. & Yano, M. DNA changes tell us about rice domestication. Curr. Opin. Plant Biol. 12, 185–192 (2009).
  Article CAS PubMed Google Scholar
• Freeling, M. et al. Fractionation mutagenesis and similar consequences of mechanisms removing dispensable or less-expressed DNA in plants. Curr. Opin. Plant Biol. 15, 131–139 (2012).
  Article CAS PubMed Google Scholar
• Weigel, D. Natural variation in Arabidopsis: from molecular genetics to ecological genomics. Plant Physiol. 158, 2–22 (2012).
  Article CAS PubMed Google Scholar
• Hamilton, J. P. & Buell, C. R. Advances in plant genome sequencing. Plant J. 70, 177–190 (2012).
  Article CAS PubMed Google Scholar
• Feuillet, C. & Eversole, K. Plant science. Solving the maze. Science 326, 1071–1072 (2009).
  Article CAS PubMed Google Scholar
• Doi, K., Yasui, H. & Yoshimura, A. Genetic variation in rice. Curr. Opin. Plant Biol. 11, 144–148 (2008).
  Article CAS PubMed Google Scholar
• Huang, X. et al. A map of rice genome variation reveals the origin of cultivated rice. Nature 490, 497–501 (2012). This is an example of the scale of analysis that is now possible using modern sequencing technology. Sequencing data from hundreds of accessions of wild and domesticated rice has made high-resolution genome-wide association studies (GWASs) for many agronomic traits in cultivated and wild rice possible.
  Article CAS PubMed PubMed Central Google Scholar
• Xu, X. et al. Resequencing 50 accessions of cultivated and wild rice yields markers for identifying agronomically important genes. Nature Biotech. 30, 105–111 (2012).
  Article CAS Google Scholar
• He, Z. et al. Two evolutionary histories in the genome of rice: the roles of domestication genes. PLoS Genet. 7, e1002100 (2011).
  Article CAS PubMed PubMed Central Google Scholar
• Kloeckener-Gruissem, B. & Freeling, M. Transposon-induced promoter scrambling: a mechanism for the evolution of new alleles. Proc. Natl Acad. Sci. USA 92, 1836–1840 (1995).
  Article CAS PubMed PubMed Central Google Scholar
• Greene, B., Walko, R. & Hake, S. Mutator insertions in an intron of the maize knotted1 gene result in dominant suppressible mutations. Genetics 138, 1275–1285 (1994).
  CAS PubMed PubMed Central Google Scholar
• Bharathan, G. et al. Homologies in leaf form inferred from KNOXI gene expression during development. Science 296, 1858–1860 (2002).
  Article CAS PubMed Google Scholar
• Salvi, S. et al. Toward positional cloning of Vgt1, a QTL controlling the transition from the vegetative to the reproductive phase in maize. Plant Mol. Biol. 48, 601–613 (2002).
  Article CAS PubMed Google Scholar
• Salvi, S. et al. Conserved noncoding genomic sequences associated with a flowering-time quantitative trait locus in maize. Proc. Natl Acad. Sci. USA 104, 11376–11381 (2007). This is the first demonstration that insertion of a TE into a conserved non-coding sequence can affect an agronomically important trait. This analysis also demonstrates that even TE insertions that are distant from plant genes can have important effects on gene expression.
  Article CAS PubMed PubMed Central Google Scholar
• Chia, J. M. et al. Maize HapMap2 identifies extant variation from a genome in flux. Nature Genet. 44, 803–807 (2012). This paper provides a comprehensive view of extant genetic variation in maize and relates it to variation in agronomically important traits in a species that has an order of magnitude more genetic diversity than humans. Because of the density of the data now available, this analysis makes it possible for high-resolution GWASs to be carried out in maize for the first time.
  Article CAS PubMed Google Scholar
• Freeling, M. & Subramaniam, S. Conserved noncoding sequences (CNSs) in higher plants. Curr. Opin. Plant Biol. 12, 126–132 (2009).
  Article CAS PubMed Google Scholar
• Liu, S. et al. Mu transposon insertion sites and meiotic recombination events co-localize with epigenetic marks for open chromatin across the maize genome. PLoS Genet. 5, e1000733 (2009).
  Article PubMed PubMed Central CAS Google Scholar
• Vollbrecht, E. et al. Genome-wide distribution of transposed Dissociation elements in maize. Plant Cell 22, 1667–1685 (2010).
  Article CAS PubMed PubMed Central Google Scholar
• Pan, X., Li, Y. & Stein, L. Site preferences of insertional mutagenesis agents in Arabidopsis. Plant Physiol. 137, 168–175 (2005).
  Article CAS PubMed PubMed Central Google Scholar
• Naito, K. et al. Unexpected consequences of a sudden and massive transposon amplification on rice gene expression. Nature 461, 1130–1134 (2009). This study demonstrates that rapid and recent amplification of a family of TEs can have substantial effects on expression of nearby genes by introducing stress-responsiveness. It also provides evidence that MITEs may have adapted to minimize the negative effects of transposition by avoiding insertion into exons.
  Article CAS PubMed Google Scholar
• Dooner, H. K., Robbins, T. P. & Jorgensen, R. A. Genetic and developmental control of anthocyanin biosynthesis. Annu. Rev. Genet. 25, 173–199 (1991).
  Article CAS PubMed Google Scholar
• Selinger, D. A. & Chandler, V. L. Major recent and independent changes in levels and patterns of expression have occurred at the b gene, a regulatory locus in maize. Proc. Natl Acad. Sci. USA 96, 15007–15012 (1999).
  Article CAS PubMed PubMed Central Google Scholar
• Selinger, D. A. & Chandler, V. L. B-Bolivia, an allele of the maize b1 gene with variable expression, contains a high copy retrotransposon-related sequence immediately upstream. Plant Physiol. 125, 1363–1379 (2001).
  Article CAS PubMed PubMed Central Google Scholar
• Walker, E. L., Robbins, T. P., Bureau, T. E., Kermicle, J. & Dellaporta, S. L. Transposon-mediated chromosomal rearrangements and gene duplications in the formation of the maize R-r complex. EMBO J. 14, 2350–2363 (1995).
  Article CAS PubMed PubMed Central Google Scholar
• Butelli, E. et al. Retrotransposons control fruit-specific, cold-dependent accumulation of anthocyanins in blood oranges. Plant Cell 24, 1242–1255 (2012). This paper provides an example of the programmatic changes that can be introduced by TE insertion. In this case, insertion of a retroelement provided both cold inducibility and tissue specificity.
  Article CAS PubMed PubMed Central Google Scholar
• Studer, A., Zhao, Q., Ross-Ibarra, J. & Doebley, J. Identification of a functional transposon insertion in the maize domestication gene tb1. Nature Genet. 43, 1160–1163 (2011). This paper demonstrates that a key mutation permitting domestication of maize involved a retroelement insertion many kilobases upstream of a gene that enhanced that gene's expression.
  Article CAS PubMed Google Scholar
• Mhiri, C. et al. The promoter of the tobacco Tnt1 retrotransposon is induced by wounding and by abiotic stress. Plant Mol. Biol. 33, 257–266 (1997).
  Article CAS PubMed Google Scholar
• Ivashuta, S. et al. Genotype-dependent transcriptional activation of novel repetitive elements during cold acclimation of alfalfa (Medicago sativa). Plant J. 31, 615–627 (2002).
  Article CAS PubMed Google Scholar
• Ito, H. et al. An siRNA pathway prevents transgenerational retrotransposition in plants subjected to stress. Nature 472, 115–119 (2011).
  Article CAS PubMed Google Scholar
• Grandbastien, M. et al. Stress activation and genomic impact of Tnt1 retrotransposons in Solanaceae. Cytogenet. Genome Res. 110, 229–241 (2005).
  Article CAS PubMed Google Scholar
• Buchmann, R. C., Asad, S., Wolf, J. N., Mohannath, G. & Bisaro, D. M. Geminivirus AL2 and L2 proteins suppress transcriptional gene silencing and cause genome-wide reductions in cytosine methylation. J. Virol. 83, 5005–5013 (2009).
  Article CAS PubMed PubMed Central Google Scholar
• Wang, Q. & Dooner, H. K. Dynamic evolution of bz orthologous regions in the Andropogoneae and other grasses. Plant J. 72, 212–221 (2012).
  Article CAS PubMed Google Scholar
• Swigonova, Z. et al. Close split of sorghum and maize genome progenitors. Genome Res. 14, 1916–1923 (2004).
  Article CAS PubMed PubMed Central Google Scholar
• Yu, C., Zhang, J. & Peterson, T. Genome rearrangements in maize induced by alternative transposition of reversed ac/ds termini. Genetics 188, 59–67 (2011).
  Article CAS PubMed PubMed Central Google Scholar
• Navarro, A. & Barton, N. H. Chromosomal speciation and molecular divergence—accelerated evolution in rearranged chromosomes. Science 300, 321–324 (2003).
  Article CAS PubMed Google Scholar
• Guillen, Y. & Ruiz, A. Gene alterations at Drosophila inversion breakpoints provide prima facie evidence for natural selection as an explanation for rapid chromosomal evolution. BMC Genomics 13, 53 (2012).
  Article PubMed PubMed Central Google Scholar
• Joron, M. et al. Chromosomal rearrangements maintain a polymorphic supergene controlling butterfly mimicry. Nature 477, 203–206 (2011).
  Article CAS PubMed PubMed Central Google Scholar
• Lowry, D. B. & Willis, J. H. A widespread chromosomal inversion polymorphism contributes to a major life-history transition, local adaptation, and reproductive isolation. PLoS Biol. 8, e1000500 (2010).
  Article PubMed PubMed Central CAS Google Scholar
• Ammiraju, J. S. et al. Dynamic evolution of Oryza genomes is revealed by comparative genomic analysis of a genus-wide vertical data set. Plant Cell 20, 3191–3209 (2008).
  Article CAS PubMed PubMed Central Google Scholar
• Hurwitz, B. L. et al. Rice structural variation: a comparative analysis of structural variation between rice and three of its closest relatives in the genus Oryza. Plant J. 63, 990–1003 (2010).
  Article CAS PubMed Google Scholar
• 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, 1262–1269 (2006).
  Article CAS PubMed PubMed Central Google Scholar
• Vielle-Calzada, J. P. et al. The Palomero genome suggests metal effects on domestication. Science 326, 1078 (2009).
  Article CAS PubMed Google Scholar
• Ledford, H. Halfway point for 1,001 genomes quest. Nature 477, 14 (2011).
  Article CAS PubMed Google Scholar
• Hu, T. T. et al. The Arabidopsis lyrata genome sequence and the basis of rapid genome size change. Nature Genet. 43, 476–481 (2011).
  Article PubMed CAS Google Scholar
• Woodhouse, M. R., Pedersen, B. & Freeling, M. Transposed genes in Arabidopsis are often associated with flanking repeats. PLoS Genet. 6, e1000949 (2010).
  Article PubMed PubMed Central CAS Google Scholar
• Yang, S. et al. Repetitive element-mediated recombination as a mechanism for new gene origination in Drosophila. PLoS Genet. 4, e3 (2008).
  Article PubMed PubMed Central CAS Google Scholar
• Bhutkar, A., Russo, S. M., Smith, T. F. & Gelbart, W. M. Genome-scale analysis of positionally relocated genes. Genome Res. 17, 1880–1887 (2007).
  Article CAS PubMed PubMed Central Google Scholar
• Abrouk, M. et al. Grass microRNA gene paleohistory unveils new insights into gene dosage balance in subgenome partitioning after whole-genome duplication. Plant Cell 24, 1776–1792 (2012).
  Article CAS PubMed PubMed Central Google Scholar
• van der Knaap, E., Sanyal, A., Jackson, S. A. & Tanksley, S. D. High-resolution fine mapping and fluorescence in situ hybridization analysis of sun, a locus controlling tomato fruit shape, reveals a region of the tomato genome prone to DNA rearrangements. Genetics 168, 2127–2140 (2004).
  Article CAS PubMed PubMed Central Google Scholar
• Xiao, H., Jiang, N., Schaffner, E., Stockinger, E. J. & van der Knaap, E. A retrotransposon-mediated gene duplication underlies morphological variation of tomato fruit. Science 319, 1527–1530 (2008). This study provides the first evidence in plants that retrotransposon-mediated retrotransposition can result in functional reprogramming patterns of gene expression.
  Article CAS PubMed Google Scholar
• Freeling, M. et al. Many or most genes in Arabidopsis transposed after the origin of the order Brassicales. Genome Res. 18, 1924–1937 (2008).
  Article CAS PubMed PubMed Central Google Scholar
• Wang, Y. H. & Warren, J. T. Jr. Mutations in retrotransposon AtCOPIA4 compromises resistance to Hyaloperonospora parasitica in Arabidopsis thaliana. Genet. Mol. Biol. 33, 135–140 (2010).
  Article CAS PubMed PubMed Central Google Scholar
• Yi, H. & Richards, E. J. A cluster of disease resistance genes in Arabidopsis is coordinately regulated by transcriptional activation & RNA silencing. Plant Cell 19, 2929–2939 (2007).
  Article CAS PubMed PubMed Central Google Scholar
• Jiang, N., Bao, Z., Zhang, X., Eddy, S. R. & essler, S. R. Pack-MULE transposable elements mediate gene evolution in plants. Nature 431, 569–573 (2004). In this paper, it is shown that TEs can capture, duplicate and combine thousands of gene fragments in rice, raising the possibility that TEs may be an important source of new genes in plants.
  Article CAS PubMed Google Scholar
• Juretic, N., Hoen, D. R., Huynh, M. L., Harrison, P. M. & Bureau, T. E. The evolutionary fate of MULE-mediated duplications of host gene fragments in rice. Genome Res. 15, 1292–1297 (2005).
  Article CAS PubMed PubMed Central Google Scholar
• Hanada, K. et al. The functional role of pack-MULEs in rice inferred from purifying selection and expression profile. Plant Cell 21, 25–38 (2009).
  Article CAS PubMed PubMed Central Google Scholar
• Du, C., Fefelova, N., Caronna, J., He, L. & Dooner, H. K. The polychromatic Helitron landscape of the maize genome. Proc. Natl Acad. Sci. USA 106, 19916–19921 (2009).
  Article CAS PubMed PubMed Central Google Scholar
• Wang, W. et al. High rate of chimeric gene origination by retroposition in plant genomes. Plant Cell 18, 1791–1802 (2006).
  Article CAS PubMed PubMed Central Google Scholar
• Muehlbauer, G. J. et al. A hAT superfamily transposase recruited by the cereal grass genome. Mol. Genet. Genom. 275, 553–563 (2006).
  Article CAS Google Scholar
• Hudson, M. E., Lisch, D. R. & Quail, P. H. The FHY3 and FAR1 genes encode transposase-related proteins involved in regulation of gene expression by the phytochrome A-signaling pathway. Plant J. 34, 453–471 (2003).
  Article CAS PubMed Google Scholar
• Li, G. et al. Coordinated transcriptional regulation underlying the circadian clock in Arabidopsis. Nature Cell Biol. 13, 616–622 (2011).
  Article CAS PubMed Google Scholar
• Lin, R. et al. Transposase-derived transcription factors regulate light signaling in Arabidopsis. Science 318, 1302–1305 (2007). This is the first demonstration that a plant transposase can take on a new functional role as a transcription factor. This study also showed that a family of exapted transposases has a key role in light signalling in plants.
  Article CAS PubMed PubMed Central Google Scholar
• Ouyang, X. et al. Genome-wide binding site analysis of FAR-RED ELONGATED HYPOCOTYL3 reveals its novel function in Arabidopsis development. Plant Cell 23, 2514–2535 (2011).
  Article CAS PubMed PubMed Central Google Scholar
• Joly-Lopez, Z., Forczek, E., Hoen, D. R., Juretic, N. & Bureau, T. E. A. Gene family derived from transposable elements during early angiosperm evolution has reproductive fitness benefits in Arabidopsis thaliana. PLoS Genet. 8, e1002931 (2012).
  Article CAS PubMed PubMed Central Google Scholar
• Cowan, R. K., Hoen, D. R., Schoen, D. J. & Bureau, T. E. MUSTANG is a novel family of domesticated transposase genes found in diverse angiosperms. Mol. Biol. Evol. 22, 2084–2089 (2005).
  Article CAS PubMed Google Scholar
• Bundock, P. & Hooykaas, P. An Arabidopsis hAT-like transposase is essential for plant development. Nature 436, 282–284 (2005).
  Article CAS PubMed Google Scholar
• Donoghue, M. T., Keshavaiah, C., Swamidatta, S. H. & Spillane, C. Evolutionary origins of Brassicaceae specific genes in Arabidopsis thaliana. BMC Evol. Biol. 11, 47 (2011).
  Article CAS PubMed PubMed Central Google Scholar
• Charlesworth, B., Borthwick, H., Bartolome, C. & Pignatelli, P. Estimates of the genomic mutation rate for detrimental alleles in Drosophila melanogaster. Genetics 167, 815–826 (2004).
  Article CAS PubMed PubMed Central Google Scholar
• Brookfield, J. F. The ecology of the genome — mobile DNA elements and their hosts. Nature Rev. Genet. 6, 128–136 (2005).
  Article CAS PubMed Google Scholar
• Lisch, D. Epigenetic regulation of transposable elements in plants. Annu. Rev. Plant Biol. 60, 43–66 (2009).
  Article CAS PubMed Google Scholar
• Slotkin, R. K. & Martienssen, R. Transposable elements and the epigenetic regulation of the genome. Nature Rev. Genet. 8, 272–285 (2007).
  Article CAS PubMed Google Scholar
• Kinoshita, Y. et al. Control of FWA gene silencing in Arabidopsis thaliana by SINE-related direct repeats. Plant J. 49, 38–45 (2007).
  Article CAS PubMed Google Scholar
• Fujimoto, R. et al. Evolution and control of imprinted FWA genes in the genus Arabidopsis. PLoS Genet. 4, e1000048 (2008).
  Article PubMed PubMed Central CAS Google Scholar
• Jeddeloh, J. A., Stokes, T. L. & Richards, E. J. Maintenance of genomic methylation requires a SWI2/SNF2-like protein. Nature Genet. 22, 94–97 (1999).
  Article CAS PubMed Google Scholar
• Saze, H. & Kakutani, T. Heritable epigenetic mutation of a transposon-flanked Arabidopsis gene due to lack of the chromatin-remodeling factor DDM1. EMBO J. 26, 3641–3652 (2007).
  Article CAS PubMed PubMed Central Google Scholar
• Liu, J. He, Y., Amasino, R. & Chen, X. siRNAs targeting an intronic transposon in the regulation of natural flowering behavior in Arabidopsis. Genes Dev. 18, 2873–2878 (2004).
  Article CAS PubMed PubMed Central Google Scholar
• Strange, A. et al. Major-effect alleles at relatively few loci underlie distinct vernalization and flowering variation in Arabidopsis accessions. PLoS ONE 6, e19949 (2011).
  Article CAS PubMed PubMed Central Google Scholar
• Lister, R. et al. Highly integrated single-base resolution maps of the epigenome in Arabidopsis. Cell 133, 523–536 (2008).
  Article CAS PubMed PubMed Central Google Scholar
• Gehring, M., Bubb, K. L. & Henikoff, S. Extensive demethylation of repetitive elements during seed development underlies gene imprinting. Science 324, 1447–1451 (2009).
  Article CAS PubMed PubMed Central Google Scholar
• Zemach, A. et al. Local DNA hypomethylation activates genes in rice endosperm. Proc. Natl Acad. Sci. USA 107, 18729–18734 (2010).
  Article CAS PubMed PubMed Central Google Scholar
• Kashkush, K., Feldman, M. & Levy, A. A. Transcriptional activation of retrotransposons alters the expression of adjacent genes in wheat. Nature Genet. 33, 102–106 (2003). This paper shows that read-out transcription from retroelements in plants can have substantial effects on gene expression. It also demonstrates that naturally occurring variation in methylation of retroelements can result in differences in expression and tissue specificity of genes.
  Article CAS PubMed Google Scholar
• Jiang, N., Jordan, I. K. & Wessler, S. R. Dasheng and RIRE2. A nonautonomous long terminal repeat element and its putative autonomous partner in the rice genome. Plant Physiol. 130, 1697–1705 (2002).
  Article CAS PubMed PubMed Central Google Scholar
• Ammiraju, J. S. et al. Evolutionary dynamics of an ancient retrotransposon family provides insights into evolution of genome size in the genus Oryza. Plant J. 52, 342–351 (2007).
  Article CAS PubMed Google Scholar
• Kashkush, K. & Khasdan, V. Large-scale survey of cytosine methylation of retrotransposons and the impact of readout transcription from long terminal repeats on expression of adjacent rice genes. Genetics 177, 1975–1985 (2007).
  Article CAS PubMed PubMed Central Google Scholar
• He, G. et al. Global epigenetic and transcriptional trends among two rice subspecies and their reciprocal hybrids. Plant Cell 22, 17–33 (2010).
  Article CAS PubMed PubMed Central Google Scholar
• Hollister, J. D. & Gaut, B. S. Epigenetic silencing of transposable elements: a trade-off between reduced transposition and deleterious effects on neighboring gene expression. Genome Res. 19, 1419–1428 (2009).
  Article CAS PubMed PubMed Central Google Scholar
• Hollister, J. D. et al. Transposable elements and small RNAs contribute to gene expression divergence between Arabidopsis thaliana and Arabidopsis lyrata. Proc. Natl Acad. Sci. USA 108, 2322–2327 (2011). Evidence is provided in this paper that silencing of TEs near genes can result in an overall reduction in gene expression. This suggests that although there is a benefit to silencing TEs, there is also a substantial potential cost, and it raises the possibility that TEs can have global effects on host gene function.
  Article CAS PubMed PubMed Central Google Scholar
• Lu, C. et al. Miniature inverted-repeat transposable elements (MITEs) have been accumulated through amplification bursts and play important roles in gene expression and species diversity in Oryza sativa. Mol. Biol. Evol. 29, 1005–1017 (2012).
  Article CAS PubMed Google Scholar
• Furbank, R. T. & Tester, M. Phenomics—technologies to relieve the phenotyping bottleneck. Trends Plant Sci. 16, 635–644 (2011).
  Article CAS PubMed Google Scholar
• Brachi, B., Morris, G. P. & Borevitz, J. O. Genome-wide association studies in plants: the missing heritability is in the field. Genome Biol. 12, 232 (2011).
  Article PubMed PubMed Central Google Scholar
• Van de Peer, Y., Fawcett, J. A., Proost, S., Sterck, L. & Vandepoele, K. The flowering world: a tale of duplications. Trends Plant Sci. 14, 680–688 (2009).
  Article CAS PubMed Google Scholar
• Treangen, T. J. & Salzberg, S. L. Repetitive DNA and next-generation sequencing: computational challenges and solutions. Nature Rev. Genet. 13, 36–46 (2012).
  Article CAS Google Scholar
• Tarailo-Graovac, M. & Chen, N. Using RepeatMasker to identify repetitive elements in genomic sequences. Curr. Protoc. Bioinformatics 25, 4.10.1–4.10.14 (2009).
  Google Scholar