Epigenetics and plant evolution
Version of Record online: 23 JUN 2005
Volume 168, Issue 1, pages 81–91, October 2005
How to Cite
Rapp, R. A. and Wendel, J. F. (2005), Epigenetics and plant evolution. New Phytologist, 168: 81–91. doi: 10.1111/j.1469-8137.2005.01491.x
- Issue online: 23 JUN 2005
- Version of Record online: 23 JUN 2005
- Received: 3 March 2005 Accepted: 13 May 2005
- 2003. Genes duplicated by polyploidy show unequal contributions to the transcriptome and organ-specific reciprocal silencing. Proceedings of the National Academy of Sciences, USA 100: 4649–4654. , , , .
- 2004. Organ-specific silencing of duplicated genes in a newly synthesized cotton allotetraploid. Genetics 168: 2217–2226. , , .
- 2000. Use of matrix attachment regions (MARs) to minimize transgene silencing. Plant Molecular Biology 43: 361–376. , , .
- 2001. Surveying CpG methylation at 5′-CCGG in the genomes of rice cultivars. Plant Molecular Biology 45: 31–39. .
- 2002. Plant epigenetics. Current Biology 12: R412. .
- 2000. Transposable element contributions to plant gene and genome evolution. Plant Molecular Biology 42: 251–269. .
- 1999. A mammalian protein with specific demethylase activity for mCpG DNA. Nature 397: 579–583. , , , .
- 2005. Dosage balance in gene regulation: biological implications. Trends in Genetics 21: 219–226. , , , .
- 2004. Functional divergence of duplicated genes formed by polyploidy during Arabidopsis evolution. Plant Cell 16: 1679–1691. , .
- 2003. From DNA structure to gene expression: mediators of nuclear compartmentalization and dynamics. Chromosome Research 11: 435–445. , , , , .
- 2002. The Argonaute family: tentacles that reach into RNAi, developmental control, stem cell maintenance, and tumorigenesis. Genes and Development 16: 2733–2742. , , , .
- 2002. Analysis of DNA methylation in Arabidopsis thaliana based on methylation-sensitive AFLP markers. Molecular Genetics and Genomics 268: 543–552. , , .
- 1999. Epistasis and the evolution of additive genetic variance in populations that pass through a bottleneck. Evolution 53: 1009–1018. , , , , , , , .
- 1996. S-Adenosylmethionine and methylation. Federation of American Societies for Experimental Biological Journal 10: 471–480. , , , , , , .
- 2002. Breakthrough of the year: small RNAs make a big splash. Science 298: 2296–2297. .
- 2004. Cryptic trysts, genomic mergers, and plant speciation. New Phytologist 161: 133–142. , .
- 2001. Ancient asymmetries in the evolution of flowers. Current Biology 11: 1050–1052. , , .
- 1999. An epigenetic mutation responsible for natural variation in floral symmetry. Nature 401: 157–161. , , .
- 1859. On the origin of species by means of natural selection, or the preservation of favoured races in the struggle for life. London, UK: W. Clowes and Sons. .
- 1998. DNA methylation in plants. Annual Review of Plant Physiology and Plant Molecular Biology 49: 223–247. , , , .
- 1999. Preservation of duplicate genes by complementary, degenerative mutations. Genetics 151: 1531–1545. , , , , , .
- 2002. Interphase chromosomes in Arabidopsis are organized as well defined chromocenters from which euchromatin loops emanate. Proceedings of the National Academy of Sciences, USA 99: 14584–14589. , , , , .
- 2002. Distribution of 5-methylcytosine residues in 5S rRNA genes in Arabidopsis thaliana and Secale cereale. Molecular Genetics and Genomics 268: 510–517. , , .
- 2005. Arabidopsis epigenetics: when RNA meets chromatin. Current Opinion in Plant Biology 8: 142–147. , .
- 1997. Mutagenic and epigenetic effects of DNA methylation. Mutation Research 386: 107–118. , .
- 1988. Epistasis and the effect of founder events on the additive genetic variance. Evolution 42: 441–454. .
- 1981. Plant speciation. New York, USA: Columbia. .
- 2003. Heterochromatin and epigenetic control of gene expression. Science 301: 798–802. , .
- 2005. Hybrid speciation in plants: new insights from molecular studies. New Phytologist 165: 411–423. , .
- 2003. Chromatin remodeling and human disease. Current Opinion in Genetics and Development 13: 246–252. , , .
- 1994. The changing concept of epigenetics. Annals of the New York Academy of Science 981: 82–96. , .
- 2001. Translating the histone code. Science 293: 1074–1080. , .
- 2002. Interplay between two epigenetic marks: DNA methylation and histone H3 lysine 9 methylation. Current Biology 12: 1360–1367. , , .
- 2004. Epialleles via DNA methylation: consequences for plant evolution. Trends in Ecology and Evolution 19: 309–314. , .
- 2003. Arabidopsis MET1 cytosine methyltransferase mutants. Genetics 163: 1109–1122. , , , , , , , , .
- 2003. Transcriptional activation of retrotransposons alters the expression of adjacent genes in wheat. Nature Genetics 33: 102–106. , , .
- 2003. Role of CG and non-CG methylation in immobilization of transposons in Arabidopsis. Current Biology 13: 421–426. , , , , .
- 2001. Dicer functions in RNA interference and in synthesis of small RNA involved in developmental timing in C. elegans. Genes and Development 15: 2654–2659. , , , , , .
- 2005. The developmental role of microRNA in plants. Current Opinion in Plant Biology 8: 38–44. , .
- 2001. Stability and inheritance of methylation states at PstI sites in Pisum. Molecular Genetics and Genomics 265: 497–507. , .
- 2002. 3D structure of the human genome: order in randomness. Chromosoma 111: 321–331. , , , , , , , , .
- 1999. Plant retrotransposons. Annual Review of Genetics 33: 479–532. , .
- 1993. The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14. Cell 75: 843–854. , , .
- 2004. Genetic and epigenetic reprogramming of the wheat genome upon allopolyploidization. Biological Journal of the Linnean Society 82: 607–613. , .
- 2003. Structure and nucleic-acid binding of the Drosophila Argonaute 2 PAZ domain. Nature 426: 465–469. , , , .
- 2001. Polyploid formation in cotton is not accompanied by rapid genomic changes. Genome 43: 874–880. , , , , .
- 1999. DNA methylation changes in rice induced by Zizania latifolia Griseb. DNA introgression. Hereditas 131: 75–78. , , , , , .
- 1998a. Rapid genomic changes in newly synthesized amphiploids of Triticum and Aegilops. II. Changes in low-copy coding DNA sequences. Genome 41: 535–542. , , .
- 1998b. Rapid genomic changes in newly synthesized amphiploids of Triticum and Aegilops. I. Changes in low-copy non-coding DNA sequences. Genome 41: 272–277. , , , , , .
- 2003. Epigenetic phenomena and the evolution of plant allopolyploids. Molecular Phylogenetics and Evolution 29: 365–379. , .
- 2002. Non-Mendelian phenomena in allopolyploid genome evolution. Current Genomics 3: 489–506. , .
- 2000. The evolutionary fate and consequences of duplicate genes. Science 290: 1151–1155. , .
- 2000. The probability of duplicate gene preservation by subfunctionalization. Genetics 154: 459–473. , .
- 2001. The probability of preservation of a newly arisen gene duplicate. Genetics 159: 1789–1804. , , , .
- 2002. Remodeling of DNA methylation and phenotypic and transcriptional changes in synthetic Arabidopsis allotetraploids. Plant Physiology 129: 733–746. , , , , , .
- 2005. Genomic changes in synthetic Arabidopsis polyploids. Plant Journal 41: 221–230. , , , , , , , .
- 1970. Evolution by gene duplication. New York, USA: Springer-Verlag. .
- 2004. Flowering time divergence and genomic rearrangements in resynthesized Brassica polyploids (Brassicaceae). Biological Journal of the Linnean Society 82: 675–688. , , , , , , .
- 2001. Histone methylation versus histone acetylation: new insights into epigenetic regulation. Current Opinion in Cell Biology 13: 263–273. , .
- 2002. The control of natural variation in cytosine methylation in Arabidopsis. Genetics 162: 355–363. , .
- 1997. Hybrid origins of plant species. Annual Review of Ecology and Systematics 28: 359–389. .
- 2004. Plant speciation – rise of the poor cousins. New Phytologist 161: 3–8. , .
- 2000. DNA methylation in health and disease. Nature Reviews Genetics 1: 11–19. , .
- 2005. The Arabidopsis HOMOLOGY-DEPENDENT GENE SILENCING1 gene codes for an S-adenosyl-L-homocysteine hydrolase required for DNA methylation-dependent gene silencing. Plant Cell 17: 404–417. , , , , , , , , , .
- 2003. Epigenetic silencing may aid evolution by gene duplication. Journal of Molecular Evolution 56: 718–729. , .
- 2003. Evolutionary change in flowers and inflorescences: evidence from naturally occurring terata. Trends in Plant Science 8: 76–82. , .
- 2004. Genome-wide in silico mapping of scaffold/matrix attachment regions in Arabidopsis suggests correlation of intragenic scaffold/matrix attachment regions with gene expression. Plant Physiology 135: 715–722. , , , , , .
- 2003. The establishment, inheritance, and function of silenced chromatin in Saccharomyces cerevisiae. Annual Review of Biochemistry 72: 481–516. , , .
- 2005. Genetic and epigenetic consequences of recent hybridization and polyploidy in Spartina (Poaceae). Molecular Ecology 14: 1163–1175. , , .
- 2000. Novel flowering time variation in the resynthesized polyploid Brassica napus. Journal of Heredity 91: 242–246. , .
- 2004. Silencing in Arabidopsis T-DNA transformants: the predominant role of a gene-specific RNA sensing mechanism versus position effects. Plant Cell 16: 2561–2572. , , , , , .
- 2001. Sequence elimination and cytosine methylation are rapid and reproducible responses of the genome to wide hybridization and allopolyploidy in wheat. Plant Cell 13: 1749–1759. , , , , .
- 1995. Rapid genome change in synthetic polyploids of Brassica and its implications for polyploid evolution. Proceedings of the National Academy of Sciences, USA 92: 7719–7723. , , , .
- 2004. The function of nuclear architecture: a genetic approach. Annual Review of Genetics 38: 305–345. , , , .
- 2003. Trimethylated lysine 9 of histone H3 is a mark for DNA methylation in Neurospora crassa. Nature Genetics 34: 75–79. , , , , , , , , .
- 2002. Evolutionary conservation of chromosome territory arrangements in cell nuclei from higher primates. Proceedings of the National Academy of Sciences, USA 99: 4424–4425. , , , , , , , , .
- 2004. DNA and histone methylation in plants. Trends in Genetics 20: 244–251. , .
- 2005. Reversible histone acetylation and deacetylation mediate genome-wide, promoter-dependent and locus-specific changes in gene expression during plant development. Genetics 169: 337–345. , , , , , , .
- 2000. Histone acetylation and an epigenetic code. Bioessays 22: 836–845. .
- 2005. Paralogs in polyploids: one for all and all for one. Plant Cell 17: 4–11. .
- 2004a. Stochastic and epigenetic changes of gene expression in Arabidopsis polyploids. Genetics 167: 1961–1973. , , , , , , , , , .
- 2004b. DNA methylation polymorphism in a set of elite rice cultivars and its possible contribution to inter-cultivar differential gene expression. Cellular and Molecular Biology Letters 9: 543–556. , , , , .
- 2003. Polyploidy and the evolutionary history of cotton. Advances in Agronomy 78: 139–186. , .
- 2005. Polyploidy and evolution in plants. In: HenryRJ, ed. Plant diversity and evolution. Wallingford, UK: CABI Publishing, 97–117. , .