Feng S. Epigenetic reprogramming in plant and animal development. Science. 2010;330:622–7.
Article
CAS
PubMed
PubMed Central
Google Scholar
Zemach A, McDaniel IE, Silva P, Zilberman D. Genome-wide evolutionary analysis of eukaryotic DNA methylation. Science. 2010;328:916–9.
Article
CAS
PubMed
Google Scholar
Niederhuth CE, Bewick AJ, Ji L, Alabady MS, Kim KD, Li Q, et al. Widespread natural variation of DNA methylation within angiosperms. Genome Biol. 2016;17:194.
Article
PubMed
PubMed Central
CAS
Google Scholar
Takuno S, Ran J-H, Gaut BS. Evolutionary patterns of genic DNA methylation vary across land plants. Nat Plants. 2016;2:15222.
Article
CAS
PubMed
Google Scholar
Das OP, Messing J. Variegated phenotype and developmental methylation changes of a maize allele originating from epimutation. Genetics. 1994;136:1121–41.
CAS
PubMed
PubMed Central
Google Scholar
Bender J, Fink GR. Epigenetic control of an endogenous gene family is revealed by a novel blue fluorescent mutant of Arabidopsis. Cell. 1995;83:725–34.
Article
CAS
PubMed
Google Scholar
Melquist S, Bender J. Transcription from an upstream promoter controls methylation signaling from an inverted repeat of endogenous genes in Arabidopsis. Genes Dev. 2003;17:2036–47.
Article
CAS
PubMed
PubMed Central
Google Scholar
Ong-Abdullah M, Ordway JM, Jiang N, Ooi S-E, Kok S, Sarpan N, et al. Loss of Karma transposon methylation underlies the mantled somaclonal variant of oil palm. Nature. 2015;525:533–7.
Article
CAS
PubMed
PubMed Central
Google Scholar
Banks JA, Masson P, Fedoroff N. Molecular mechanisms in the developmental regulation of the maize Suppressor-Mutator transposable element. Genes Dev. 1988;2:1364–80.
Article
CAS
PubMed
Google Scholar
Jacobsen SE. Hypermethylated SUPERMAN epigenetic alleles in Arabidopsis. Science. 1997;277:1100–3.
Article
CAS
PubMed
Google Scholar
Soppe WJJ, Jacobsen SE, Alonso-Blanco C, Jackson JP, Kakutani T, Koornneef M, et al. The late flowering phenotype of fwa mutants is caused by gain-of-function epigenetic alleles of a homeodomain gene. Mol Cell. 2000;6:791–802.
Article
CAS
PubMed
Google Scholar
Stam M, Belele C, Dorweiler JE, Chandler VL. Differential chromatin structure within a tandem array 100 kb upstream of the maize b1 locus is associated with paramutation. Genes Dev. 2002;16:1906–18.
Article
CAS
PubMed
PubMed Central
Google Scholar
Colot V, Maloisel L, Rossignol JL. Interchromosomal transfer of epigenetic states in Ascobolus: transfer of DNA methylation is mechanistically related to homologous recombination. Cell. 1996;86:855–64.
Article
CAS
PubMed
Google Scholar
Stokes TL, Kunkel BN, Richards EJ. Epigenetic variation in Arabidopsis disease resistance. Genes Dev. 2002;16:171–82.
Article
CAS
PubMed
PubMed Central
Google Scholar
Quadrana L, Almeida J, Asis R, Duffy T, Dominguez PG, Bermúdez L, et al. Natural occurring epialleles determine vitamin E accumulation in tomato fruits. Nat Commun. 2014;5:3027.
Article
CAS
PubMed
Google Scholar
Reinders J, Wulff BBH, Mirouze M, Mari-Ordóñez A, Dapp M, Rozhon W, et al. Compromised stability of DNA methylation and transposon immobilization in mosaic Arabidopsis epigenomes. Genes Dev. 2009;23:939–50.
Article
CAS
PubMed
PubMed Central
Google Scholar
Johannes F, Porcher E, Teixeira FK, Saliba-Colombani V, Simon M, Agier N, et al. Assessing the impact of transgenerational epigenetic variation on complex traits. PLoS Genet. 2009;5:e1000530.
Article
PubMed
PubMed Central
CAS
Google Scholar
Roux F, Colomé-Tatché M, Edelist C, Wardenaar R, Guerche P, Hospital F, et al. Genome-wide epigenetic perturbation jump-starts patterns of heritable variation found in nature. Genetics. 2011;188:1015–7.
Article
CAS
PubMed
PubMed Central
Google Scholar
Eichten SR, Schmitz RJ, Springer NM. Epigenetics: beyond chromatin modifications and complex genetic regulation. Plant Physiol. 2014;165:933–47.
Article
CAS
PubMed
PubMed Central
Google Scholar
Silveira AB, Trontin C, Cortijo S, Barau J, Del Bem LEV, Loudet O, et al. Extensive natural epigenetic variation at a de novo originated gene. PLoS Genet. 2013;9:3–10.
Article
CAS
Google Scholar
Tsukahara S, Kobayashi A, Kawabe A, Mathieu O, Miura A, Kakutani T. Bursts of retrotransposition reproduced in Arabidopsis. Nature. 2009;461:423–6.
Article
CAS
PubMed
Google Scholar
Mirouze M, Reinders J, Bucher E, Nishimura T, Schneeberger K, Ossowski S, et al. Selective epigenetic control of retrotransposition in Arabidopsis. Nature. 2009;461:1–5.
Article
CAS
Google Scholar
Miura A, Yonebayashi S, Watanabe K, Toyama T, Shimada H, Kakutani T. Mobilization of transposons by a mutation abolishing full DNA methylation in Arabidopsis. Nature. 2001;411:212–4.
Article
CAS
PubMed
Google Scholar
Singer T, Yordan C, Martienssen RA. Robertson’s Mutator transposons in A. thaliana are regulated by the chromatin-remodeling gene Decrease in DNA Methylation (DDM1). Genes Dev. 2001;15:591–602.
Article
CAS
PubMed
PubMed Central
Google Scholar
Cheng C, Tarutani Y, Miyao A, Ito T, Yamazaki M, Sakai H, et al. Loss of function mutations in the rice chromomethylase OsCMT3a cause a burst of transposition. Plant J. 2015;83:1069–81.
Article
CAS
PubMed
Google Scholar
Kim KD, El Baidouri M, Abernathy B, Iwata-Otsubo A, Chavarro C, Gonzales M, et al. A comparative epigenomic analysis of polyploidy-derived genes in soybean and common bean. Plant Physiol. 2015;168:1433–47.
Article
CAS
PubMed
PubMed Central
Google Scholar
Maloisel L, Rossignol JL. Suppression of crossing-over by DNA methylation in Ascobolus. Genes Dev. 1998;12:1381–9.
Article
CAS
PubMed
PubMed Central
Google Scholar
Mirouze M, Lieberman-Lazarovich M, Aversano R, Bucher E, Nicolet J, Reinders J, et al. Loss of DNA methylation affects the recombination landscape in Arabidopsis. Proc Natl Acad Sci U S A. 2012;109:5880–5.
Article
CAS
PubMed
PubMed Central
Google Scholar
Colomé-Tatché M, Cortijo S, Wardenaar R, Morgado L, Lahouze B, Sarazin A, et al. Features of the Arabidopsis recombination landscape resulting from the combined loss of sequence variation and DNA methylation. Proc Natl Acad Sci U S A. 2012;109:16240–5.
Article
PubMed
PubMed Central
Google Scholar
Melamed-Bessudo C, Levy AA. Deficiency in DNA methylation increases meiotic crossover rates in euchromatic but not in heterochromatic regions in Arabidopsis. Proc Natl Acad Sci U S A. 2012;109:E981–8.
Article
CAS
PubMed
PubMed Central
Google Scholar
Yelina NE, Choi K, Chelysheva L, Macaulay M, de Snoo B, Wijnker E, et al. Epigenetic remodeling of meiotic crossover frequency in Arabidopsis thaliana DNA methyltransferase mutants. PLoS Genet. 2012;8:e1002844.
Article
CAS
PubMed
PubMed Central
Google Scholar
Shen H, He H, Li J, Chen W, Wang X, Guo L, et al. Genome-wide analysis of DNA methylation and gene expression changes in two Arabidopsis ecotypes and their reciprocal hybrids. Plant Cell. 2012;24:875–92.
Article
CAS
PubMed
PubMed Central
Google Scholar
Dapp M, Reinders J, Bédiée A, Balsera C, Bucher E, Theiler G, et al. Heterosis and inbreeding depression of epigenetic Arabidopsis hybrids. Nat Plants. 2015;1:15092.
Article
CAS
PubMed
Google Scholar
Rigal M, Becker C, Pélissier T, Pogorelcnik R, Devos J, Ikeda Y, et al. Epigenome confrontation triggers immediate reprogramming of DNA methylation and transposon silencing in Arabidopsis thaliana F1 epihybrids. Proc Natl Acad Sci U S A. 2016;113:E2083–92.
Article
CAS
PubMed
PubMed Central
Google Scholar
Lauss K, Wardenaar R, van Hulten MHA, Guryev V, Keurentjes JJB, Stam M, et al. Epigenetic divergence is sufficient to trigger heterosis in Arabidopsis thaliana. bioRxiv. 2016; doi:http://dx.doi.org/10.1101/059980.
Groszmann M, Greaves IK, Fujimoto R, Peacock WJ, Dennis ES. The role of epigenetics in hybrid vigour. Trends Genet. 2013;29:684–90.
Article
CAS
PubMed
Google Scholar
Chen ZJ. Genomic and epigenetic insights into the molecular bases of heterosis. Nat Rev Genet. 2013;14:471–82.
Article
CAS
PubMed
Google Scholar
Kirkbride RC, Yu HH, Nah G, Zhang C, Shi X, Chen ZJ. An epigenetic role for disrupted paternal gene expression in postzygotic seed abortion in Arabidopsis interspecific hybrids. Mol Plant. 2015;8:1766–75.
Article
CAS
PubMed
Google Scholar
Fort A, Ryder P, Mckeown PC, Wijnen C, Aarts MG, Sulpice R, et al. Disaggregating polyploidy, parental genome dosage and hybridity contributions to heterosis in Arabidopsis thaliana. New Phytol. 2016;209:590–9.
Article
CAS
PubMed
Google Scholar
Groszmann M, Gonzalez-Bayon R, Lyons RL, Greaves IK, Kazan K, Peacock WJ, et al. Hormone-regulated defense and stress response networks contribute to heterosis in Arabidopsis F1 hybrids. Proc Natl Acad Sci U S A. 2015;112:E6397–406.
Article
CAS
PubMed
PubMed Central
Google Scholar
Secco D, Wang C, Shou H, Schultz MD, Chiarenza S, Nussaume L, et al. Stress induced gene expression drives transient DNA methylation changes at adjacent repetitive elements. Elife. 2015;4:e09343.
Article
PubMed Central
Google Scholar
Feil R, Fraga MF. Epigenetics and the environment: emerging patterns and implications. Nat Rev Genet. 2012;13:97–109.
CAS
PubMed
Google Scholar
Meyer P. Epigenetic variation and environmental change. J Exp Bot. 2015;66:3541–8.
Article
CAS
PubMed
Google Scholar
Zhang X. Dynamic differential methylation facilitates pathogen stress response in Arabidopsis. Proc Natl Acad Sci U S A. 2012;109:12842–3.
Article
CAS
PubMed
PubMed Central
Google Scholar
Yu A, Lepere G, Jay F, Wang J, Bapaume L, Wang Y, et al. Dynamics and biological relevance of DNA demethylation in Arabidopsis antibacterial defense. Proc Natl Acad Sci U S A. 2013;110:2389–94.
Article
CAS
PubMed
PubMed Central
Google Scholar
López Sánchez A, Stassen JH, Furci L, Smith LM, Ton J. The role of DNA (de)methylation in immune responsiveness of Arabidopsis. Plant J. 2016;88:361–74.
Article
PubMed
PubMed Central
CAS
Google Scholar
Espinas NA, Saze H, Saijo Y. Epigenetic control of defense signaling and priming in plants. Front Plant Sci. 2016;7:1201.
PubMed
PubMed Central
Google Scholar
Luna E, Ton J. The epigenetic machinery controlling transgenerational systemic acquired resistance. Plant Signal Behav. 2012;7:615–8.
Article
CAS
PubMed
PubMed Central
Google Scholar
Conrath U, Beckers GJM, Langenbach CJG, Jaskiewicz MR. Priming for enhanced defense. Annu Rev Phytopathol. 2015;53:97–119.
Article
CAS
PubMed
Google Scholar
Rapp RA, Wendel JF. Epigenetics and plant evolution. New Phytol. 2005;168:81–91.
Article
CAS
PubMed
Google Scholar
Richards EJ, Reinders J, Wulff BBH, Mirouze M. Quantitative epigenetics: DNA sequence variation need not apply. Genes Dev. 2009;23:1601–5.
Article
CAS
PubMed
PubMed Central
Google Scholar
Weigel D, Colot V. Epialleles in plant evolution. Genome Biol. 2012;13:249.
Article
CAS
PubMed
PubMed Central
Google Scholar
Diez CM, Roessler K, Gaut BS. Epigenetics and plant genome evolution. Curr Opin Plant Biol. 2014;18:1–8.
Article
CAS
PubMed
Google Scholar
Springer NM. Epigenetics and crop improvement. Trends Genet. 2013;29:241–7.
Article
CAS
PubMed
Google Scholar
Ji L, Neumann DA, Schmitz RJ. Crop epigenomics: identifying, unlocking, and harnessing cryptic variation in crop genomes. Mol Plant. 2014;8:860–70.
Article
CAS
Google Scholar
Law JA, Jacobsen SE. Establishing, maintaining and modifying DNA methylation patterns in plants and animals. Nat Rev Genet. 2010;11:204–20.
Article
CAS
PubMed
PubMed Central
Google Scholar
Stroud H, Greenberg MVC, Feng S, Bernatavichute YV, Jacobsen SE. Comprehensive analysis of silencing mutants reveals complex regulation of the Arabidopsis methylome. Cell. 2013;152:352–64.
Article
CAS
PubMed
PubMed Central
Google Scholar
Laird PW. Principles and challenges of genome-wide DNA methylation analysis. Nat Rev Genet. 2010;11:191–203.
Article
CAS
PubMed
Google Scholar
Zhang X, Yazaki J, Sundaresan A, Cokus S, Chan SWL, Chen H, et al. Genome-wide high-resolution mapping and functional analysis of DNA methylation in Arabidopsis. Cell. 2006;126:1189–201.
Article
CAS
PubMed
Google Scholar
Cokus SJ, Feng S, Zhang X, Chen Z, Merriman B, Haudenschild CD, et al. Shotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterning. Nature. 2008;452:215–9.
Article
CAS
PubMed
PubMed Central
Google Scholar
Lister R, Malley RCO, Tonti-filippini J, Gregory BD, Berry CC, Miller AH, et al. Highly integrated single-base resolution maps of the epigenome in Arabidopsis. Cell. 2008;133:523–36.
Article
CAS
PubMed
PubMed Central
Google Scholar
Zilberman D, Gehring M, Tran RK, Ballinger T, Henikoff S. Genome-wide analysis of Arabidopsis thaliana DNA methylation uncovers an interdependence between methylation and transcription. Nat Genet. 2007;39:61–9.
Article
CAS
PubMed
Google Scholar
Schmitz RJ, Schultz MD, Urich MA, Nery JR, Pelizzola M, Libiger O, et al. Patterns of population epigenomic diversity. Nature. 2013;495:193–8.
Article
CAS
PubMed
PubMed Central
Google Scholar
Gent JI, Ellis NA, Guo L, Harkess AE, Yao Y, Zhang X, et al. CHH islands: de novo DNA methylation in near-gene chromatin regulation in maize. Genome Res. 2013;23:628–37.
Article
CAS
PubMed
PubMed Central
Google Scholar
Seymour DK, Koenig D, Hagmann J, Becker C, Weigel D. Evolution of DNA methylation patterns in the Brassicaceae is driven by differences in genome organization. PLoS Genet. 2014;10:e1004785.
Article
PubMed
PubMed Central
CAS
Google Scholar
Amborella Genome Project, Albert VA, Barbazuk WB, dePamphilis CW, Der JP, Leebens-Mack J, et al. The Amborella genome and the evolution of flowering plants. Science. 2013;342:1241089.
Article
CAS
Google Scholar
Zhong S, Fei Z, Chen Y-R, Zheng Y, Huang M, Vrebalov J, et al. Single-base resolution methylomes of tomato fruit development reveal epigenome modifications associated with ripening. Nat Biotechnol. 2013;31:154–9.
Article
CAS
PubMed
Google Scholar
Alonso C, Pérez R, Bazaga P, Herrera CM. Global DNA cytosine methylation as an evolving trait: phylogenetic signal and correlated evolution with genome size in angiosperms. Front Genet. 2015;5:1–9.
Google Scholar
Cao J, Schneeberger K, Ossowski S, Günther T, Bender S, Fitz J, et al. Whole-genome sequencing of multiple Arabidopsis thaliana populations. Nat Genet. 2011;43:956–63.
Article
CAS
PubMed
Google Scholar
Gan X, Stegle O, Behr J, Steffen JG, Drewe P, Hildebrand KL, et al. Multiple reference genomes and transcriptomes for Arabidopsis thaliana. Nature. 2011;477:419–23.
Article
CAS
PubMed
PubMed Central
Google Scholar
Long Q, Rabanal FA, Meng D, Huber CD, Farlow A, Platzer A, et al. Massive genomic variation and strong selection in Arabidopsis thaliana lines from Sweden. Nat Genet. 2013;45:884–90.
Article
CAS
PubMed
PubMed Central
Google Scholar
Hagmann J, Becker C, Muller J, Stegle O, Meyer RC, Wang G, et al. Century-scale methylome stability in a recently diverged Arabidopsis thaliana lineage. PLoS Genet. 2015;11:e1004920.
Article
PubMed
PubMed Central
CAS
Google Scholar
Dubin MJ, Zhang P, Meng D, Remigereau M-S, Osborne EJ, Paolo Casale F, et al. DNA methylation in Arabidopsis has a genetic basis and shows evidence of local adaptation. Elife. 2015;4:e05255.
Article
PubMed
PubMed Central
Google Scholar
1001 Genomes Consortium. 1,135 genomes reveal the global pattern of polymorphism in Arabidopsis thaliana. Cell. 2016;166:481–91.
Article
CAS
Google Scholar
Kawakatsu T, Huang SC, Jupe F, Sasaki E, Schmitz RJ, Urich MA, et al. Epigenomic diversity in a global collection of Arabidopsis thaliana accessions. Cell. 2016;166:492–505.
Article
CAS
PubMed
Google Scholar
Becker C, Hagmann J, Müller J, Koenig D, Stegle O, Borgwardt K, et al. Spontaneous epigenetic variation in the Arabidopsis thaliana methylome. Nature. 2011;480:245–9.
Article
CAS
PubMed
Google Scholar
Schmitz RJ, Schultz MD, Lewsey MG, Malley RCO, Urich MA, Libiger O, et al. Transgenerational epigenetic instability is a source of novel methylation variants. Science. 2011;334:369–73.
Article
CAS
PubMed
PubMed Central
Google Scholar
Van der Graaf A, Wardenaar R, Neumann DA, Taudt A, Shaw RG, Jansen RC, et al. Rate, spectrum, and evolutionary dynamics of spontaneous epimutations. Proc Natl Acad Sci U S A. 2015;112:6676–81.
Article
PubMed
PubMed Central
CAS
Google Scholar
Schmitz RJ, He Y, Valdés-lópez O, Res G, Gent JI, Ellis NA, et al. Epigenome-wide inheritance of cytosine methylation variants in a recombinant inbred population. Genome Res. 2013;23:1663–74.
Article
CAS
PubMed
PubMed Central
Google Scholar
Virdi KS, Laurie JD, Xu Y-Z, Yu J, Shao M-R, Sanchez R, et al. Arabidopsis MSH1 mutation alters the epigenome and produces heritable changes in plant growth. Nat Commun. 2015;6:6386.
Article
CAS
PubMed
PubMed Central
Google Scholar
West PT, Li Q, Ji L, Eichten SR, Song J, Vaughn MW, et al. Genomic distribution of H3K9me2 and DNA methylation in a maize genome. PLoS One. 2014;9:1–10.
Google Scholar
Li Q, Eichten SR, Hermanson PJ, Zaunbrecher VM, Song J, Wendt J, et al. Genetic perturbation of the maize methylome. Plant Cell. 2014;26:4602–16.
Article
PubMed
PubMed Central
CAS
Google Scholar
Li X, Zhu C, Yeh CT, Wu W, Takacs EM, Petsch KA, et al. Genic and nongenic contributions to natural variation of quantitative traits in maize. Genome Res. 2012;22:2436–44.
Article
CAS
PubMed
PubMed Central
Google Scholar
Bennetzen JL, Wang H. The contributions of transposable elements to the structure, function, and evolution of plant genomes. Annu Rev Plant Biol. 2014;65:505–30.
Article
CAS
PubMed
Google Scholar
Wendel JF, Jackson SA, Meyers BC, Wing RA. Evolution of plant genome architecture. Genome Biol. 2016;17:37.
Article
PubMed
PubMed Central
CAS
Google Scholar
Bennetzen JL, Ma J, Devos KM. Mechanisms of recent genome size variation in flowering plants. Ann Bot. 2005;95:127–32.
Article
CAS
PubMed
PubMed Central
Google Scholar
Woo HR, Richards EJ. Natural variation in DNA methylation in ribosomal RNA genes of Arabidopsis thaliana. BMC Plant Biol. 2008;8:92.
Article
PubMed
PubMed Central
CAS
Google Scholar
Quadrana L, Bortolini Silveira A, Mayhew GF, LeBlanc C, Martienssen RA, Jeddeloh JA, et al. The Arabidopsis thaliana mobilome and its impact at the species level. Elife. 2016;5:e15716.
Article
PubMed
PubMed Central
Google Scholar
Stuart T, Eichten SR, Cahn J, Karpievitch Y, Borevitz JO, Lister R. Population scale mapping of novel transposable element diversity reveals links to gene regulation and epigenomic variation. bioRxiv. 2016; doi: http://dx.doi.org/10.1101/039511.
Mari-Ordóñez A, Marchais A, Etcheverry M, Martin A, Colot V, Voinnet O. Reconstructing de novo silencing of an active plant retrotransposon. Nat Genet. 2013;45:1029–39.
Article
PubMed
CAS
Google Scholar
Hollister JD, Gaut BS. Epigenetic silencing of transposable elements: a trade-off between reduced transposition and deleterious effects on neighboring gene expression. Genome Res. 2009;19:1419–28.
Article
CAS
PubMed
PubMed Central
Google Scholar
Ahmed I, Sarazin A, Bowler C, Colot V, Quesneville H. Genome-wide evidence for local DNA methylation spreading from small RNA-targeted sequences in Arabidopsis. Nucleic Acids Res. 2011;39:6919–31.
Article
CAS
PubMed
PubMed Central
Google Scholar
Taudt A, Colomé-Tatché M, Johannes F. Genetic sources of population epigenomic variation. Nat Rev Genet. 2016;17:319–32.
Article
CAS
PubMed
Google Scholar
Eichten SR, Briskine R, Song J, Li Q, Swanson-Wagner R, Hermanson PJ, et al. Epigenetic and genetic influences on DNA methylation variation in maize populations. Plant Cell. 2013;25:2783–97.
Article
CAS
PubMed
PubMed Central
Google Scholar
Stroud H, Do T, Du J, Zhong X, Feng S, Johnson L, et al. Non-CG methylation patterns shape the epigenetic landscape in Arabidopsis. Nat Struct Mol Biol. 2014;21:64–72.
Article
CAS
PubMed
Google Scholar
Hu L, Li N, Xu C, Zhong S, Lin X, Yang J, et al. Mutation of a major CG methylase in rice causes genome-wide hypomethylation, dysregulated genome expression, and seedling lethality. Proc Natl Acad Sci U S A. 2014;111:10642–7.
Article
CAS
PubMed
PubMed Central
Google Scholar
Bewick AJ, Ji L, Niederhuth CE, Willing E-M, Hofmeister BT, Shi X, et al. On the origin and evolutionary consequences of gene body DNA methylation. Proc Natl Acad Sci U S A. 2016;113:9111–6.
Article
CAS
PubMed
PubMed Central
Google Scholar
Lindroth AM, Cao X, Jackson JP, Zilberman D, McCallum CM, Henikoff S, et al. Requirement of CHROMOMETHYLASE3 for maintenance of CpXpG methylation. Science. 2001;292:2077–80.
Article
CAS
PubMed
Google Scholar
Shen X, De Jonge J, Forsberg SKG, Pettersson ME, Sheng Z, Hennig L, et al. Natural CMT2 variation is associated with genome-wide methylation changes and temperature seasonality. PLoS Genet. 2014;10:e1004842.
Article
PubMed
PubMed Central
CAS
Google Scholar
Jullien PE, Susaki D, Yelagandula R, Higashiyama T, Berger F. DNA methylation dynamics during sexual reproduction in Arabidopsis thaliana. Curr Biol. 2012;22:1825–30.
Article
CAS
PubMed
Google Scholar
Papa CM, Springer NM, Muszynski MG, Meeley R, Kaeppler SM. Maize chromomethylase Zea methyltransferase2 is required for CpNpG methylation. Plant Cell. 2001;13:1919–28.
Article
CAS
PubMed
PubMed Central
Google Scholar
Matzke MA, Kanno T, Matzke AJM. RNA-directed DNA methylation: the evolution of a complex epigenetic pathway in flowering plants. Annu Rev Plant Biol. 2014;66:1–25.
Google Scholar
Bewick AJ, Niederhuth CE, Rohr NA, Griffin PT, Leebens-Mack J, Schmitz RJ. The evolution of CHROMOMETHYLASES and gene body DNA methylation in plants. bioRxiv. 2016; doi: http://dx.doi.org/10.1101/054924.
Willing E-M, Rawat V, Mandáková T, Maumus F, James GV, Nordström KJV, et al. Genome expansion of Arabis alpina linked with retrotransposition and reduced symmetric DNA methylation. Nat Plants. 2015;1:14023.
Article
CAS
PubMed
Google Scholar
Takuno S, Gaut BS. Body-methylated genes in Arabidopsis thaliana are functionally important and evolve slowly. Mol Biol Evol. 2012;29:219–27.
Article
CAS
PubMed
Google Scholar
Takuno S, Gaut BS. Gene body methylation is conserved between plant orthologs and is of evolutionary consequence. Proc Natl Acad Sci U S A. 2013;110:1797–802.
Article
CAS
PubMed
PubMed Central
Google Scholar
Genereux DP, Miner BE, Bergstrom CT, Laird CD. A population-epigenetic model to infer site-specific methylation rates from double-stranded DNA methylation patterns. Proc Natl Acad Sci U S A. 2005;102:5802–7.
Article
CAS
PubMed
PubMed Central
Google Scholar
Meng D, Dubin M, Zhang P, Osborne EJ, Stegle O, Clark RM, et al. Limited contribution of DNA methylation variation to expression regulation in Arabidopsis thaliana. PLoS Genet. 2016;12:e1006141.
Article
PubMed
PubMed Central
CAS
Google Scholar
Cubas P, Vincent C, Coen E. An epigenetic mutation responsible for natural variation in floral symmetry. Nature. 1999;401:157–61.
Article
CAS
PubMed
Google Scholar
Manning K, Tör M, Poole M, Hong Y, Thompson AJ, King GJ, et al. A naturally occurring epigenetic mutation in a gene encoding an SBP-box transcription factor inhibits tomato fruit ripening. Nat Genet. 2006;38:948–52.
Article
CAS
PubMed
Google Scholar
Eichten SR, Swanson-Wagner RA, Schnable JC, Waters AJ, Hermanson PJ, Liu S, et al. Heritable epigenetic variation among maize inbreds. PLoS Genet. 2011;7:e1002372.
Article
CAS
PubMed
PubMed Central
Google Scholar
Jiang C, Mithani A, Belfield EJ, Mott R, Hurst LD, Harberd NP. Environmentally responsive genome-wide accumulation of de novo Arabidopsis thaliana mutations and epimutations. Genome Res. 2014;24:1821–9.
Article
CAS
PubMed
PubMed Central
Google Scholar
Verhoeven KJF, Jansen JJ, van Dijk PJ, Biere A. Stress-induced DNA methylation changes and their heritability in asexual dandelions. New Phytol. 2010;185:1108–18.
Article
CAS
PubMed
Google Scholar
Shaw RG, Byers DL, Darmo E. Spontaneous mutational effects on reproductive traits of Arabidopsis thaliana. Genetics. 2000;155:369–78.
CAS
PubMed
PubMed Central
Google Scholar
Kawashima T, Berger F. Epigenetic reprogramming in plant sexual reproduction. Nat Rev Genet. 2014;15:613–24.
Article
CAS
PubMed
Google Scholar
Ossowski S, Schneeberger K, Lucas-Lledó JI, Warthmann N, Clark RM, Shaw RG, et al. The rate and molecular spectrum of spontaneous mutations in Arabidopsis thaliana. Science. 2010;327:92–4.
Article
CAS
PubMed
Google Scholar
Becker C, Weigel D. Epigenetic variation: origin and transgenerational inheritance. Curr Opin Plant Biol. 2012;15:562–7.
Article
CAS
PubMed
Google Scholar
Estoup A, Jarne P, Cornuet JM. Homoplasy and mutation model at microsatellite loci and their consequences for population genetics analysis. Mol Ecol. 2002;11:1591–604.
Article
CAS
PubMed
Google Scholar
Novikova PY, Hohmann N, Nizhynska V, Tsuchimatsu T, Ali J, Muir G, et al. Sequencing of the genus Arabidopsis identifies a complex history of nonbifurcating speciation and abundant trans-specific polymorphism. Nat Genet. 2016;48:1077–82.
Article
CAS
PubMed
Google Scholar
Nordborg M, Hu TT, Ishino Y, Jhaveri J, Toomajian C, Zheng H, et al. The pattern of polymorphism in Arabidopsis thaliana. PLoS Biol. 2005;3:1289–99.
Article
CAS
Google Scholar
Wright S. Evolution in mendelian populations. Genetics. 1931;16:97–159.
CAS
PubMed
PubMed Central
Google Scholar
Song YS, Steinrücken M. A simple method for finding explicit analytic transition densities of diffusion processes with general diploid selection. Genetics. 2012;190:1117–29.
Article
PubMed
PubMed Central
Google Scholar
Charlesworth B, Jain K. Purifying selection, drift, and reversible mutation with arbitrarily high mutation rates. Genetics. 2014;198:1587–602.
Article
PubMed
PubMed Central
Google Scholar
Wang J, Fan C. A neutrality test for detecting selection on DNA methylation using single methylation polymorphism frequency spectrum. Genome Biol Evol. 2014;7:154–71.
Article
PubMed
PubMed Central
CAS
Google Scholar
Kimura M. The number of heterozygous nucleotide sites maintained in a finite population due to steady flux of mutations. Genetics. 1969;61:893–903.
CAS
PubMed
PubMed Central
Google Scholar
Wakeley J, Aliacar N. Gene genealogies in a metapopulation. Genetics. 2001;159:893–905.
CAS
PubMed
PubMed Central
Google Scholar
Abramowitz M, Stegun IA. Handbook of mathematical functions. New York: Dover; 1965.
Google Scholar
Živković D, Steinrücken M, Song YS, Stephan W. Transition densities and sample frequency spectra of diffusion processes with selection and variable population size. Genetics. 2015;200:601–17.
Article
PubMed
PubMed Central
Google Scholar