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The genomes and transposable elements in plants: are they friends or foes?

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Abstract

Transposable elements (TEs) are mobile genetic elements that are present in prokaryotes and eukaryotes. The ubiquity and abundance of these self-replicating entities, bereft of cellular function, had earned them the label of ‘genomic parasites’. However, the status of TEs has been revised, with ample genomic and biological evidence now portraying them as “genomic gold”. They are perceived as a major participant in the evolution of species. This review addresses the classification of TEs as well as their role and significance in the evolution of genomes, genetic diversity, gene regulation, and exaptation of contemporary species of the plant and animal kingdoms.

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References

  • Abrusán G, Sziláyi A, Zhang Y, Papp B (2013) Turning gold into ‘junk’: transposable elements utilize central proteins of cellular networks. Nucl Acids Res 41: 3190–3200

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Ågren J, Wright SI (2011) Co-evolution between transposable elements and their host: a major factor in genome evolution? Chromosome Res 19:777–786

    Article  PubMed  CAS  Google Scholar 

  • Alzohairy AM, Gyulai GG, Jansen RK, Bahieldin A (2013) Transposable elements domesticated and neofunctionalization by eukaryotic genomes. Plasmid 69:1–15

    Article  CAS  PubMed  Google Scholar 

  • Bartoš J, Paux E, Kofler R, Havránková M, Kopechy D, Suchánkoá P, Šimková H, Šafár J, Town CD, Lelley T et al (2008) A first survey of the rye (Secale cereale) genome composition through BAC end sequencing pf the short arm of chromosome 1R. BMC Plant Biol 8:95

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Belyayev A, Kalendar R, Brodsky L, Nevo E, Schulman AH, Raskina O (2010) Transposable elements in a marginal plant population: temporal fluctuations provide new insights into genome evolution of wild diploid wheat. Mobile DNA 1:6. doi:10.1186/1759-8753-1-6

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Bennett M, Leitch IJ (2011) Nuclear DNA amounts in angiosperms: targets, trends, and tomorrow. Ann Bot 107:467–590

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Bennett M, Leitch IJ (2012) Plant DNA C-value database (release 6.0. December 2012)

  • Bennetzen JL, Ma J, Devos KM (2005) Mechanisms of recent genome size variation in flowering plants. Ann Bot 95:127–132

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Bhattacharyya MK, Smith AM, Ellis TH, Hedley C, Martin C (1990) 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

    Article  CAS  PubMed  Google Scholar 

  • Blumenstiel JP (2011) Evolutionary dynamics of transposable elements in a small RNA world. Trends Genet 27:23–31

    Article  CAS  PubMed  Google Scholar 

  • Bossdorf P, Richards CL, Pigliucci M (2008) Epigenetics for ecologists. Ecol Lett 11:106–115

    PubMed  Google Scholar 

  • Bowers JE, Chapman BA, Rong J, Paterson AH (2003) Unravelling angiosperm genome evolution by phylogenetic analysis of chromosomal duplication events. Nature 422:433–438

    Article  CAS  PubMed  Google Scholar 

  • Brunet TDP, Doolittle WF (2015) Multilevel selection theory and evolutionary functions of transposable elements. Genome Biol Evol 7:2445–2457

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Bundock P, Hooykaas P (2005) An Arabidopsis hAT-like transposase is essential for plant development. Nature 436:282–284

    Article  CAS  PubMed  Google Scholar 

  • Canapa A, Barucca M, Biscotti MA, Forconi M, Olmo E (2016) Transposons, genome size, and evolutionary insights in animals. Cytogenet Genome Res 147:217–239

    Article  Google Scholar 

  • Chadha S, Sharma M (2014) Transposable elements as stress adaptive capacitors induce genomic instability in fungal pathogen Magnaporthe oryzae. PLOS Genet 9(4): e94415 doi:10.1371/journal.pone.0094415

    Article  CAS  Google Scholar 

  • Chen W, VanOpdorp N, Fitzl D, Tewari J, Friedmann P, Greene T, Thomson S, Kumpatla S, Zheng P (2012) Transposon insertion in a cinnamyl alcohol dehydrogenase gene is responsible for a brown midrib1 mutation in maize. Plant Mol Biol 80:289–297

    Article  CAS  PubMed  Google Scholar 

  • Civán P, Švec M, Hauptvogel P (2011) On the coevolution of transposable elements and plant genomes. J Bot Article ID 893546. doi:10.1155/2011/893546

    Google Scholar 

  • Cowan R, Hoen D, Scoen D, Bureau T (2005) MUSTANG is a novel family of domesticated transposase genes found in diverse angiosperms. Mol Biol Evol 22:2084–2089

    Article  CAS  PubMed  Google Scholar 

  • Devos KM, Brown JKM, Bennetzen JL (2002) Genome size reduction through illegitimate recombination. Genome Res 12:1075–1079

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Donoghue MTA, Keshavaiah C, Swamidatta SH, Spillane C (2011) Evolutionary origins of Brassicaceae specific genes in Arabidopsis thaliana. BMC Evol Biol 11:47. doi:10.1186/1471-2148-11-47

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Doolittle WF, Sapienza C (1980) Selfish genes, the phenotype paradigm and genome evolution. Nature 284:601–603

    Article  CAS  PubMed  Google Scholar 

  • Dooner HK, Robbins TP (1991) Genetic and developmental control of anthocyanin biosynthesis. Annu Rev Genet 25:173–199

    Article  CAS  PubMed  Google Scholar 

  • Du C, Fefelova N, Caronna J, He L, Dooner HK (2009) The polychromatic Helitron landscape of the maize genome. Proc Natl Acad Sci USA 106:19916–19921

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Estep MC, DeBarry JD, Bennetzen JL (2013) The dynamics of LTR retrotransposon accumulation across 25 million years of panicoid grass evolution. Heredity 110:194–204

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Fedoroff NV (2012) Transposable elements, epigenetics, and genome evolution. Science 338:758–767

    Article  CAS  PubMed  Google Scholar 

  • Fedoroff NV, Bennetzen JL (2013) Transposons, genome shock, and genome evolution. In “Plant transposons and genome dynamics in evolution”. First Edition, NV Fedoroff ed. Wiley, Hoboken pp 181–201

  • Feschotte C, Prtiham EJ (2005) Non-mammalian c-integrase are encoded by giant transposable elements. Trends Genet 21:551–552

    Article  CAS  PubMed  Google Scholar 

  • Feschotte C, Prtiham EJ (2007) DNA transposons and the evolution of eukaryotic genomes. Ann Rev Genet 41:331–368

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Finnegan DJ (1989) Eukaryotic transposable elements and genome evolution. Trends Genet 5:103–107

    Article  CAS  PubMed  Google Scholar 

  • Gao Y, Liu H, An C, Shi Y, Liu X, Yuan W, Zhang B, Yang J, Yu C, Gao H (2013) Arabidopsis FRS4/CPD25 and FHY3/CPD45 work cooperatively to promote the expression of the chloroplast division gene ARC5 and chloroplast division. Plant J 75:795–807

    Article  CAS  PubMed  Google Scholar 

  • Goodwin T, Butler ML, Poulter RT (2003) Cryptons: a group of tyrosine-recombinase-encoding DNA transposons from pathogenic fungi. Microbiology 149:3099–3109

    Article  CAS  PubMed  Google Scholar 

  • Gould SJ, Eldredge N (1977) Punctuated equilibria: the tempo and mode of evolution reconsidered. Paleobiology 3:115–151

    Article  Google Scholar 

  • Gould SJ, Vrba ES (1982) Exaptation-a missing term in the science of form. Paleobiology 8:4–15

    Article  Google Scholar 

  • Gregory TR (2001) Coincidence, coevolution, or causation? DNA content, cell size, and C-value enigma. Biol Rev 76:65–101

    Article  CAS  PubMed  Google Scholar 

  • Gregory TR (2002) A bird’s-eye view of the C-value enigma: genome size, cell size, and metabolic rate in the class Aves. Evol Int J org Evol 56:121–130

    Article  CAS  Google Scholar 

  • Greilhuber J, Doležel J, Lysák, Bennett M (2005) The origin, evolution, and proposed stabilization of the term ‘genome size’ and ‘C-value’ to describe nuclear DNA contents. Ann Bot 95:255–260

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Gupta S, Gallavotti A, Stryker GA, Schmidt RJ, Lal SK (2005) A novel class of Helitron-related transposable elements in maize contains portions of multiple pseudogenes. Plant Mol Biol 57:115–127

    Article  CAS  PubMed  Google Scholar 

  • Hawkins JS, Kim H, Nason JD, Wendel JF (2006) Differential lineage-specific amplification of transposable elements is responsible for genome size variation in Gossypium. Genome Res 16:1252–1261

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Hawkins JS, Grover CE, Wendel JF (2008) Repeated big bangs and the expanding universe: directionality in plant genome evolution. Plant Sci 174:557–562

    Article  CAS  Google Scholar 

  • Hawkins JS, Proulx SR, Rapp RA, Wendel JF (2009) Rapid DNA loss as a counterbalance to genome expansion through retrotransposon proliferation in plants. Proc Natl Acad Sci USA 106:17811–17816

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Hickman AB, Chandler M, Dyda F (2010) Integrating prokaryotes and eukaryotes: DNA transposases in light of structure. Crit Rev Biochem Mol Biol 45:50–69

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Hoen D, Bureau D (2012) Transposable element exaptation in plants. In “Plant transposable elements” Grandbastien MA, Casacuberta JM (eds). Springer Berlin pp 219–251

  • Hoen D, Bureau D (2015) Discovery of novel genes derived from transposable elements using integrative genomic analysis. Mol Biol Evol 32:1487–1506

    Article  CAS  PubMed  Google Scholar 

  • Hollister JD, Gaut BS (2009) Epigenetic silencing of transposable elements: A trade-off between reduced transposition and deleterious effects on neighboring gene expression. Genome Res 19:1419–1428

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Hollister JD, Smith LM, Guo YL, Ott F, Weigel D, Gaut BS (2011) Transposable elements and small RNAs contribute to gene expression divergence between Arabidopsis thaliana and Arabidopsis lyrata. Proc Natl Acad Sci USA 108:2322–2327

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Hu T, Patty P, Bakker EG, Cao J, Cheng JF, Clark RM, Fahlgren N, Fawcett JA, Grimwood J, Gundlach H et al (2011) The Arabidopsis lyrata genome sequence and the basis of rapid genome size change. Nature Genet 43:476–481

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Hua-Van A, Rouzic AL, Boutin TS, Filée J, Capy P (2011) The struggle for life of the genome’s selfish architects. Biol Direct 6:19

    Article  PubMed  PubMed Central  Google Scholar 

  • Javidfar F, Cheng B (2013) Construction of a genetic linkage map and QTL analysis of erucic acid content and glucosinolate components in yellow mustard (Sinapis alba L.). BMC Plant Biol 13:142

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Joly-Lopez Z, Forczek E, Hoen DR, Jurec N, Bureau TE (2012) A gene family derived from transposable elements during early angiosperm evolution has reproductive benefits in Arabidopsis thaliana. PLoS Genet 8:e1002931

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Joly-Lopez Z, Hoen DR, Blanchette M, Bureau TE (2016) Phylogenetic and genomic analyses resolve the origin of important plant genes derived from transposable elements. Mol Biol Evol 33:1937–1956

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Jurka J, Bao WD, Kojima KK (2011) Families of transposable elements, population structure and the origin of species. Bio Direct 6:44

    Article  CAS  Google Scholar 

  • Kapitonov V, Jurka J (2003) Molecular paleontology of transposable elements in the Drosophila melanogaster genome. Proc Acad Natl Sci USA 100: 6569–6574

    Article  CAS  Google Scholar 

  • Kapitonov VV, Jurka J (2005) RAG1 core and V(D)J recombination signal sequences were derived from Transib rtransposon. PLoS Biol 3:e181

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Kapitonov V, Jurka J (2006) Self-synthesizing DNA transposons in eukaryotes. Proc Natl Acad Sci USA 103:440–4545

    Article  CAS  Google Scholar 

  • Kaul S, Koo HL, Jenkins J, Rizzo M, Rooney T, Tallon LJ, Feldblyum T, Nierman W, Benito MI, Town CD et al (2000) Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408:796–815

    Article  CAS  Google Scholar 

  • Kawase M, Fukunaga K, Kato K (2005) Diverse origins of waxy foxtail millet crops in East and Southeast Asia mediated by multiple transposable element insertions. Mol Gen Genomic 27$: 131–140.

    Article  CAS  Google Scholar 

  • Kellis M, Birren BW, Lander ES (2004) Proof and evolutionary analysis of ancient genome duplication in the yeast Saccharomyces cerevisiae. Nature 428:617–624

    Article  CAS  PubMed  Google Scholar 

  • Knight CA, Molinari NA, Petrov DA (2005) The large genome constrain hypothesis: evolution, ecology, and phenotype. Ann Bot 95:177–190

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Kobayashi S, Goto-Yamamoto N, Hirochika H (2004) Retrotransposon-induced mutations in grape skin color. Science 304:982

    Article  PubMed  Google Scholar 

  • Kojima KK, Jurka J (2011) Crypton transposons: identification of new diverse families and ancient domesticated events. Mobile DNA 2: 12

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Kovach A, Wegrzyn J, Parra G, Holt C, Bruening GE, Loosptra CA, Hartigan J, Yandell M, Langley CH, Korf I, Neale DB (2010) The Pinus taeda genome is characterized by diverse and highly diverged repetitive sequences. BMC Genomics 11: 420 doi:10.1186/1471-2164-11-420

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Kumar A, Benntzen JL (1999) Plant retrotransposable elements. Ann Rev Genet 33:479–532

    Article  CAS  PubMed  Google Scholar 

  • Lai J, Li Y, Messing J, Dooner HK (2005) Gene movement by Helitron transposons contributes to the haplotype variability of maize. Proc Natl Acad Sci USA 102:9068

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Lal SK, Giroux MJ, Brendel V, Vallejos CE, Hannah LC (2003) The maize genome contains a Helitron insertion. Plant Cell 15:381–391

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Le Rouzic A, Boutin TS, Capy P (2007) Long-term evolution of transposable elements. Proc Natl Acad Sci USA 49:19375–19380

    Article  Google Scholar 

  • Lee SI, Kim NS (2014) Transposable elements and genome size variations in plants. Genom Inform 12: 87–97

    Article  Google Scholar 

  • Levin HL (2002) Newly identified retrotransposons of Ty3/gypsy class in fungi, plants, and vertebrates. In: “Mobile DNA II” N. Craig et al (ed) edited. ASM Press, Washington DC, pp 684–701

  • Levy AA (2013) Transposons in plant speciation. In “Plant transposons and genome dynamics in evolution”. First Edition, NV Fedoroff edited. Wiley, Hoboken, pp 165–179

  • Li Y, Dooner HK (2009) Excision of Helitron transposons in maize. Genetics 182:399–402

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Li G, Siddiqui H, Teng Y, Lin R, Wan XY, Li J, Lau OS, Ouyang X, Dai M, Wan J et al (2011) Coordinated transcriptional regulation underlying the circadian clock in Arabidopsis. Nat Cell Biol 13:616–622

    Article  CAS  PubMed  Google Scholar 

  • Liang SS, Hartwig B, Perera P, Mora-Garcia S, de Leau E, Thorton H, de Alves FL, Rapsilber J, Yang S, James GV et al (2016) Kicking against the PRCs—A domesticated transposase silencing mediated by polycomb group proteins and is accessory component of polycomb repressive complex2. PloS Genet 12: e1005812. doi:10.1371/journal.pgen.1005812

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Lin R, Wang H (2004) Arabidopsis FHY3/FAR1 gene family and distinct roles of its members in light control of Arabidopsis development. Plant Physiol 136:4010–4022

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Lin R, Ding L, Casola C, Ripoll DR, Feschotte C, Wang H (2007) Transposase-derived transcription factors regulate light signaling in Arabidopsis. Science 318:1302–1305

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Lira-Medeiros CF, Parisod C, Fernandes RA, Mata CS, Cardoso MA, Ferreira PCG (2010) Epigenetic variation in mangrove plants occurring in contrasting natural environment. PLoS ONE. doi: 10.1371/journal.pone.0010326

    PubMed  PubMed Central  Google Scholar 

  • Lisch D (2013a) How important are transposons for plant evolution? Nat Rev Genet 14:49–61

    Article  CAS  PubMed  Google Scholar 

  • Lisch D (2013b) Transposons in plant gene regulation. In “Plant transposons and genome dynamics in evolution”. First Edition, NV Fedoroff edited. Wiley, Hoboken, pp 93–116

  • Lönnig W-E, Saedler H (2002) Chromosome rearrangements and transposable elements. Ann Rev Genet 36:389–410

    Article  PubMed  CAS  Google Scholar 

  • Makarevitch I, Waters AJ, West PT, Stitzere M, Hirsh CN, Ross-Ibarra J, Springer NM (2015) Transposable elements contribute to activation of genes I response to heat stress. PLOS Genet 11: e1005566. doi:10.1371/journal.pgen.1005566

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Martienssen R, Chandler V (2013) Molecular mechanisms of transposon epigenetic regulation. In “Plant transposons and genome dynamics in evolution”. First Edition, NV Fedoroff edited. Wiley, Hoboken, pp 71–92

  • McClintock B (1948) Mutable loci in maize. Carnegie Institute of Washington Year Book 47; 155–169

  • McClintock B (1956) Controlling elements and the gene. Cold Spring Harb Quant Biol 21:: 197–216

    Article  CAS  Google Scholar 

  • McClintock B (1984) The significance of responses of the genome to challenge. Science 226:792–801

    Article  CAS  PubMed  Google Scholar 

  • Megallon S, Sanderson M (2005) Angiosperm divergence times: the effect of genes, codon positions, and time constraints. Evol Int J org Evol 59:1653–1670

    Article  Google Scholar 

  • Miller WJ, Hagemann S, Reiter E, Pinsker W (1992) P-element homologous sequences are tandemly repeated in the genome of Drosphila guanche. Proc Natl Acad Sci USA 89:4018–4022

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Mirouze and Paszkowski J (2011) Epigenetic contribution to stress adaptation in plants. Curr Opin Plant Biol 14:267–274

    Article  CAS  PubMed  Google Scholar 

  • Morgante M, Brunner S, Pea G, Fengler K, Azuccolo A, Rafalski A (2005) Gene duplication and exon shuffling by helitron-like transposons generate intraspecific diversity in maize. Nature Genet 37:997–1002

    Article  CAS  PubMed  Google Scholar 

  • Muehlhauber GJ, Bhau BS, Syed NH, Heinen S, Cho S, Marshall D, Pateyron S, Buisine N, Chalhoub B, Flavell AJ (2006) A hAT superfamily transposase recruited by the cereal grass genome. Mol Genet Genom 275: 553–563

    Article  CAS  Google Scholar 

  • Moutri AR, Marchetto MCN, Coufal NG, Gage FH (2007) The necessary junk: new functions for transposable elements. Hum Mol Genet 16:R159–R167

    Article  CAS  Google Scholar 

  • Nystedt B, Street NR, Wetterbom A, Zuccolo A, Lin YC, Scofield DG, Vezzi F, Delhomme N, Giacomello S, Alexeyyenko A et al (2013) The Norway spruce genome sequence and conifer genome evolution. Nature 495:579–584

    Article  CAS  Google Scholar 

  • Oliver KR, Greene WK (2009) Transposable elements: powerful facilitators of evolution. Bioessays 31:703–714

    Article  CAS  PubMed  Google Scholar 

  • Oliver KR, Greene WK (2012) Transposable elements and viruses as factors in adaptation and evolution: an expansion and strengthening of the TR-Thrust hypothesis. Ecol Evol 12:2912–2933

    Article  Google Scholar 

  • Oliver KR, McComb JA, Greene W (2013) Transposable elements: powerful contributors to angiosperm evolution and diversity. Genome Biol 5:1886–1901

    Article  Google Scholar 

  • Ono R, Nakamura K, Inoue K, Naruse M, Usami T, Wakisaka-Saito N, Hino T, Suzuki-Migishima R, Ogonuki N, Miki H et al (2006) Deletion of Peg10, an imprinted gene acquired from a retrotransposon, causes early embryonic lethality. Nat Genet 38:101–106

    Article  CAS  PubMed  Google Scholar 

  • Orgel LE, Crick FH (1980) Selfish DNA: the ultimate parasite. Nature 284:604–607

    Article  CAS  PubMed  Google Scholar 

  • Piffanelli P, Droc G, Mieulet D, Nanau N, Bes M, Bourgeois E, Rouviere C, Gavory F, Cruaud C, Ghesquiere A, Giiderdoni E (2007) Large-scale characterization of Tos17 insertion sites in a rice T0DNA mutant library. Plant Mol Biol 65:587–601

    Article  CAS  PubMed  Google Scholar 

  • Reznikoff WS (2003) Tn5 as a model or understanding DNA transposition. Mol Microbiol 47:1199–1206

    Article  CAS  PubMed  Google Scholar 

  • Rieseberg LH (1997) Hybrid origins of plant species. Ann Rev Ecol Syst 28:359–389

    Article  Google Scholar 

  • Rostoks N, Park YJ, Ramakrishma W, Ma J, Druka A, Shiloff BA, SanMiguel PJ, Jiang Z, Brueggeman R et al (2002) Genome sequencing reveals gene content, genomic organization, and recombination relationships in barley. Funct Integ. Genomics 2:70–80

    Google Scholar 

  • Schnable PS, Ware D, Fulton RS, Stein JC, Wei F, Pasternak S, Liang C, Zhang J, Fulton L, Graves TA et al (2009) The B73 maize genome: complexity, diversity, and dynamics. Science 326:1112–1115

    Article  CAS  PubMed  Google Scholar 

  • Schulman AH, Wicker T (2013) A field guide to transposable elements. In Plant Transposons and Genome Dynamics in Evolution, First edition, HV Fedoroff ed. Wiley, Hoboken. pp 15–40

  • Selinger DA, Chandler VL (1999) Major recent and independent changes in levels and patterns of expression of expression have occurred at the b gene, a regulatory locus in maize. Proc Natl Acad Sci USA 96:15007–15012

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Serra F, Becher V, Dopazo H (2013) Neutral theory predicts the relative abundance and diversity of genetic elements in a broad array of eukaryotic genomes. PLoS ONE 8(6): e63915. doi:10.1371/journal.pone.0063915

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Settles A, Holding DR, Tan BC, Latchaw SP, Liu J, Suzuki M, Li L, O’Brien BA, Fajarado DS, Wroclawska E et al (2007) Sequence-indexed mutation in maize using the UniformMu transposon-tagging population. BMC Genom 8:116

    Article  CAS  Google Scholar 

  • Slotkin RK, Martienssen R (2007) Transposable elements and epigenetic regulation of the genome. Nat Rev Genet 8:272–285

    Article  CAS  PubMed  Google Scholar 

  • Smit AF, Riggs AD (1996) Tiggers and DNA transposon fossils in the human genome. Proc Natl Acad Sci USA 93:1443–1448

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Smith JJ, Suminaya K, Amemiya C (2012) A living fossil in the genome of a living fossil: Harbinger transposons in the Coelacanth genome. Mol Biol Evol 29:985–993

    Article  CAS  PubMed  Google Scholar 

  • Smith JJ, Kuraku S, Holt C, Sauka-Spengler T, Jiang N, Campbell MS, Li W et al (2013) Sequencing of the sea lamprey (Petromyzon marinus) genome provides insights into vertebrate evolution”. Nat Genet 45:415–421

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Soltis DE, Bell CD, Kim S, Soltis PS (2008) Origin and early evolution of angiosperms. Ann NY Acad Sci 1133:3–25

    Article  CAS  PubMed  Google Scholar 

  • Staton SE, Bakken BH, Blackman BK, Chapman MA, Kane NC, Tang S, Ungerer MC, Knapp SJ, Rieseberg LH, Burker JM (2012) The sunflower (Helianthus annus L.) genome reflects a recent history of biased accumulation of transposable elements. Plant J 72: 142–153

    Article  CAS  Google Scholar 

  • Stirnberg P, Zhao S, Williamson L, Ward S, Leyser O (2012) FHY3 promotes shoot branching and stress tolerance in Arabidopsis in an AXR1-dependent manner. Plant J 71:907–920

    Article  CAS  PubMed  Google Scholar 

  • Studer A, Zhao Q, Ross-Ibarra J, Doebley J (2011) Identification of a functional transposon insertion in the maize domestication gene tb1. Nature Genet 43:1160–1163

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Tang W, Ji Q, Huang Y, Jiang Z, Bao M, Wang H, Lin R (2013) FAR-RED ELONGATED HYPOCOTYL3 and FAR-RED IMPAIRED RESPONSE1 transcription factors integrate light and abscisic acid signaling in Arabidopsis. Plant Physiol 163:857–866

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Thomas CA Jr (1971) The genetic organization of chromosomes. Ann Rev Genet 5:2237–2256

    Article  Google Scholar 

  • Thomas and Pritham (2014) Helitrons, the eukaryotic rolling-circle transposable elements. Microbiol Spect 3: 893–926.

    Google Scholar 

  • Tsuchiya T, Eulgem T (2016) An alternate polyadenylation mechanism coopted to Arabidopsis RPP7 gene through intronic retrotransposon domestication. Proc Natl Acad Sci USA 110:E3535–E3543

    Article  Google Scholar 

  • Ungerer MC, Strakosh SC, Zhen Y (2006) Genome expansion in three hybrid sunflower species is associated with retrotransposon proliferation. Curr Biol 16:R872

    Article  CAS  PubMed  Google Scholar 

  • Vicient CM, Suoniemi A, Anamthawat-Jonsson K, Tanskanen J, Beharav V, Nevo E, Schulman AH (1999) Retrotransposon BARE-1 and the role in genome evolution in the genus Hordeum. Plant Cell 11: 1769–1784

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Vitte C, Panaud O (2005) LTR retrotransposons and flowering plant genome size: emergence of the increase/decrease model. Cytogenet Genome Res 110:91–107

    Article  CAS  PubMed  Google Scholar 

  • Volff JN (2006) Turning junk into gold: domestication of transposable elements and creation of new genes in eukaryotes. Bioessays 28:913–922

    Article  CAS  PubMed  Google Scholar 

  • Voytas DF, Boeke JD (2002) Ty1 and Ty5 of Saccharomyces cereviseae. In: Craige et al (ed) edited. ASM Press, Washington, D.C, pp 631–662

    Google Scholar 

  • Wang Q, Dooner HK (2006) Remarkable variation in maize genome structure inferred from haplotype diversity at the bz locus. Proc Natl Acad Sci USA 103:17644–17649

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Wendel JF, Jackson SA, Meyers BC, Wing RA (2016) Evolution of plant genome architecture. Genome Biol 17:37. doi:10.1186/s13059-016-0908-1

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Wicker T, Sabot F, Hua-Van A, Bennetzen JL, Capy P, Chalhoub B, Flavell A, Leroy O, Morgante M, Panaud O et al (2007) A unified classification system for eukaryotic transposable elements. Nat Rev Genet 8:973–982

    Article  CAS  PubMed  Google Scholar 

  • Yang L, Bennetzen J (2009) Distribution, diversity, evolution, and survival of Helitrons in the maize genome. Proc Natl Acad Sci USA 106:19922–19927

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Zedek F, Šmerda J, Šmerda P, Bureš P (2010) Correlated evolution of LTR retrotransposons and genome size in the genus Eleocharis. BMC Plant Biol 10:265

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Zhang J, Yu C, Krishnaswamy L, Peterson T (2011) Transposable elements as catalysts for chromosome rearrangements. Methods Mol Biol 701:315–326

    Article  CAS  PubMed  Google Scholar 

  • Zhao D, Fergoson AA, Jiang N (2015) What makes up plant genomes: The vanishing line between transposable elements and genes. Biochim Biophys Acta 1859: 366–380

  • Zheng F, Cheng B (2014) Transposable element insertion and epigenetic modification cause the multiallelic variation in the expression of FAE1 in Sinapis alba. Plant Cell 26:2648–2659

    Article  CAS  Google Scholar 

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Acknowledgements

Full appreciation and indebtedness is extended to Dr. Ramesh Bhambhani for his editorial assistance with the manuscript. This study has been worked with the support of a research grant of Kangwon National University in 2016–2017.

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  1. Department of Molecular Bioscience, Kangwon National University, Chuncheon, 200-701, South Korea

    Nam-Soo Kim

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Kim, NS. The genomes and transposable elements in plants: are they friends or foes?. Genes Genom 39, 359–370 (2017). https://doi.org/10.1007/s13258-017-0522-y

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  • DOI: https://doi.org/10.1007/s13258-017-0522-y

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