| [1] | AGI (2000) Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408: 796–815.
|
| [2] | Lander ES, Linton LM, Birren B, Nusbaum C, Zody MC, et al. (2001) Initial sequencing and analysis of the human genome. Nature 409: 860–921.
|
| [3] | Doolittle WF, Sapienza C (1980) Selfish genes, the phenotype paradigm and genome evolution. Nature 284: 601–603. doi: 10.1038/284601a0
|
| [4] | Orgel LE, Crick FH (1980) Selfish DNA: the ultimate parasite. Nature 284: 604–607. doi: 10.1038/284604a0
|
| [5] | Wicker T, Sabot F, Hua-Van A, Bennetzen JL, Capy P, et al. (2007) A unified classification system for eukaryotic transposable elements. Nat Rev Genet 8: 973–982. doi: 10.1038/nrg2165
|
| [6] | Volff J-N (2006) Turning junk into gold: domestication of transposable elements and the creation of new genes in eukaryotes. Bioessays 28: 913–922. doi: 10.1002/bies.20452
|
| [7] | Feschotte C (2008) Transposable elements and the evolution of regulatory networks. Nat Rev Genet 397–405. doi: 10.1038/nrg2337
|
| [8] | Sinzelle L, Izsvak Z, Ivics Z (2009) Molecular domestication of transposable elements: From detrimental parasites to useful host genes. Cell Mol Life Sci 66: 1073–1093. doi: 10.1007/s00018-009-8376-3
|
| [9] | Volff JN (2009) Cellular genes derived from Gypsy/Ty3 retrotransposons in mammalian genomes. Ann N Y Acad Sci 1178: 233–243. doi: 10.1111/j.1749-6632.2009.05005.x
|
| [10] | Hua-Van A, Le Rouzic A, Boutin TS, Filee J, Capy P (2011) The struggle for life of the genome's selfish architects. Biology direct 6: 19. doi: 10.1186/1745-6150-6-19
|
| [11] | Feschotte C, Pritham EJ (2007) DNA transposons and the evolution of eukaryotic genomes. Annu Rev Genet 41: 331–368. doi: 10.1146/annurev.genet.40.110405.090448
|
| [12] | Whitelam GC, Johnson E, Peng J, Carol P, Anderson ML, et al. (1993) Phytochrome A null mutants of Arabidopsis display a wild-type phenotype in white light. Plant Cell 5: 757–768. doi: 10.1105/tpc.5.7.757
|
| [13] | Hudson M, Ringli C, Boylan MT, Quail PH (1999) The FAR1 locus encodes a novel nuclear protein specific to phytochrome A signaling. Genes Dev 13: 2017–2027. doi: 10.1101/gad.13.15.2017
|
| [14] | Hudson ME, Lisch DR, Quail PH (2003) 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. doi: 10.1046/j.1365-313x.2003.01741.x
|
| [15] | Bundock P, Hooykaas P (2005) An Arabidopsis hAT-like transposase is essential for plant development. Nature 436: 282–284. doi: 10.1038/nature03667
|
| [16] | Zdobnov E, Campillos M, Harrington E, Torrents D, Bork P (2005) Protein coding potential of retroviruses and other transposable elements in vertebrate genomes. Nucleic Acids Res 33: 946–954. doi: 10.1093/nar/gki236
|
| [17] | Cowan R, Hoen D, Schoen D, Bureau T (2005) MUSTANG is a novel family of domesticated transposase genes found in diverse angiosperms. Mol Biol Evol 22: 2084–2089. doi: 10.1093/molbev/msi202
|
| [18] | Muehlbauer GJ, Bhau BS, Syed NH, Heinen S, Cho S, et al. (2006) A hAT superfamily transposase recruited by the cereal grass genome. Mol Genet Genomics 275: 553–563. doi: 10.1007/s00438-006-0098-8
|
| [19] | Saccaro NL, Van Sluys M-A, de Mello Varani A, Rossi M (2007) MudrA-like sequences from rice and sugarcane cluster as two bona fide transposon clades and two domesticated transposases. Gene 392: 117–125. doi: 10.1016/j.gene.2006.11.017
|
| [20] | Piriyapongsa J, Marino-Ramirez L, Jordan IK (2007) Origin and evolution of human microRNAs from transposable elements. Genetics 176: 1323–1337. doi: 10.1534/genetics.107.072553
|
| [21] | Benjak A, Forneck A, Casacuberta JM (2008) Genome-wide analysis of the “cut-and-paste” transposons of grapevine. PLoS ONE 3: e3107 doi:10.1371/journal.pone.0003107.. doi: 10.1371/journal.pone.0003107
|
| [22] | Le QH, Wright S, Yu Z, Bureau T (2000) Transposon diversity in Arabidopsis thaliana. Proc Natl Acad Sci U S A 97: 7376–7381. doi: 10.1073/pnas.97.13.7376
|
| [23] | Yu Z, Wright SI, Bureau TE (2000) Mutator-like elements in Arabidopsis thaliana. Structure, diversity and evolution. Genetics 156: 2019–2031.
|
| [24] | Rossi M, Araujo PG, de Jesus EM, Varani AM, Van Sluys MA (2004) Comparative analysis of Mutator -like transposases in sugarcane. Molecular genetics and genomics : MGG 272: 194–203. doi: 10.1007/s00438-004-1036-2
|
| [25] | Boguski MS, Lowe TM, Tolstoshev CM (1993) dbEST–database for “expressed sequence tags”. Nat genet 4: 332–333. doi: 10.1038/ng0893-332
|
| [26] | Babu MM, Iyer LM, Balaji S, Aravind L (2006) The natural history of the WRKY-GCM1 zinc fingers and the relationship between transcription factors and transposons. Nucleic Acids Res 34: 6505–6520. doi: 10.1093/nar/gkl888
|
| [27] | Hua-Van A, Capy P (2008) Analysis of the DDE Motif in the Mutator Superfamily. J Mol Evol 67: 670–681. doi: 10.1007/s00239-008-9178-1
|
| [28] | Orr HA (2009) Fitness and its role in evolutionary genetics. Nature reviews Genetics 10: 531–539. doi: 10.1038/nrg2603
|
| [29] | Smith AM, Stitt M (2007) Coordination of carbon supply and plant growth. Plant, cell & environment 30: 1126–1149. doi: 10.1111/j.1365-3040.2007.01708.x
|
| [30] | Lin R, Ding L, Casola C, Ripoll DR, Feschotte C, et al. (2007) Transposase-derived transcription factors regulate light signaling in Arabidopsis. Science 318: 1302–1305. doi: 10.1126/science.1146281
|
| [31] | Simon SA, Meyers BC (2011) Small RNA-mediated epigenetic modifications in plants. Curr Opin Plant Biol 14: 148–155. doi: 10.1016/j.pbi.2010.11.007
|
| [32] | Lister R, O'Malley RC, Tonti-Filippini J, Gregory BD, Berry CC, et al. (2008) Highly integrated single-base resolution maps of the epigenome in Arabidopsis. Cell 133: 523–536. doi: 10.1016/j.cell.2008.03.029
|
| [33] | Zhang X, Yazaki J, Sundaresan A, Cokus S, Chan SW, et al. (2006) Genome-wide high-resolution mapping and functional analysis of DNA methylation in arabidopsis. Cell 126: 1189–1201. doi: 10.1016/j.cell.2006.08.003
|
| [34] | Gregory BD, O'Malley RC, Lister R, Urich MA, Tonti-Filippini J, et al. (2008) A link between RNA metabolism and silencing affecting Arabidopsis development. Developmental cell 14: 854–866. doi: 10.1016/j.devcel.2008.04.005
|
| [35] | de Araujo P, Rossi M, de Jesus E, Saccaro N, Kajihara D, et al. (2005) Transcriptionally active transposable elements in recent hybrid sugarcane. Plant J 44: 707–717. doi: 10.1111/j.1365-313x.2005.02579.x
|
| [36] | Jiao Y, Deng XW (2007) A genome-wide transcriptional activity survey of rice transposable element-related genes. Genome Biol 8: R28. doi: 10.1186/gb-2007-8-2-r28
|
| [37] | Ouyang X, Li J, Li G, Li B, Chen B, et al. (2011) Genome-Wide Binding Site Analysis of FAR-RED ELONGATED HYPOCOTYL3 Reveals Its Novel Function in Arabidopsis Development. Plant Cell 23: 2514–2535. doi: 10.1105/tpc.111.085126
|
| [38] | Lin R, Teng Y, Park H-J, Ding L, Black C, et al. (2008) Discrete and essential roles of the multiple domains of Arabidopsis FHY3 in mediating phytochrome A signal transduction. Plant Physiol 148: 981–992. doi: 10.1104/pp.108.120436
|
| [39] | Hoen DR, Park KC, Elrouby N, Yu Z, Mohabir N, et al. (2006) Transposon-mediated expansion and diversification of a family of ULP-like genes. Mol Biol Evol 23: 1254–1268. doi: 10.1093/molbev/msk015
|
| [40] | Cordaux R, Udit S, Batzer MA, Feschotte C (2006) Birth of a chimeric primate gene by capture of the transposase gene from a mobile element. P Natl Acad Sci U S A 103: 8101–8106. doi: 10.1073/pnas.0601161103
|
| [41] | Swarbreck D, Wilks C, Lamesch P, Berardini TZ, Garcia-Hernandez M, et al. (2008) The Arabidopsis Information Resource (TAIR): gene structure and function annotation. Nucleic acids res 36: D1009–1014. doi: 10.1093/nar/gkm965
|
| [42] | Salamov AA, Solovyev VV (2000) Ab initio gene finding in Drosophila genomic DNA. Genome Res 10: 516–522. doi: 10.1101/gr.10.4.516
|
| [43] | Tanaka T, Antonio BA, Kikuchi S, Matsumoto T, Nagamura Y, et al. (2008) The Rice Annotation Project Database (RAP-DB): 2008 update. Nucleic Acids Res 36: D1028–1033. doi: 10.1093/nar/gkm978
|
| [44] | Paterson AH, Bowers JE, Bruggmann R, Dubchak I, Grimwood J, et al. (2009) The Sorghum bicolor genome and the diversification of grasses. Nature 457: 551–556. doi: 10.1038/nature07723
|
| [45] | Marchler-Bauer A, Lu S, Anderson JB, Chitsaz F, Derbyshire MK, et al. (2011) CDD: a Conserved Domain Database for the functional annotation of proteins. Nucleic Acids Res 39: D225–229. doi: 10.1093/nar/gkq1189
|
| [46] | Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. Journal of molecular biology 215: 403–410. doi: 10.1016/s0022-2836(05)80360-2
|
| [47] | Ming R, Hou S, Feng Y, Yu Q, Dionne-Laporte A, et al. (2008) The draft genome of the transgenic tropical fruit tree papaya (Carica papaya Linnaeus). Nature 452: 991–996. doi: 10.1038/nature06856
|
| [48] | Jaillon O, Aury JM, Noel B, Policriti A, Clepet C, et al. (2007) The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla. Nature 449: 463–467. doi: 10.1038/nature06148
|
| [49] | Cannon SB, Sterck L, Rombauts S, Sato S, Cheung F, et al. (2006) Legume genome evolution viewed through the Medicago truncatula and Lotus japonicus genomes. Proceedings of the National Academy of Sciences of the United States of America 103: 14959–14964. doi: 10.1073/pnas.0603228103
|
| [50] | Goodstein DM, Shu S, Howson R, Neupane R, Hayes RD, et al. (2012) Phytozome: a comparative platform for green plant genomics. Nucleic acids research 40: D1178–1186. doi: 10.1093/nar/gkr944
|
| [51] | Schnable PS, Ware D, Fulton RS, Stein JC, Wei F, et al. (2009) The B73 maize genome: complexity, diversity, and dynamics. Science 326: 1112–1115.
|
| [52] | TIBI (2010) Genome sequencing and analysis of the model grass Brachypodium distachyon. Nature 463: 763–768.
|
| [53] | Edgar RC (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic acids research 32: 1792–1797. doi: 10.1093/nar/gkh340
|
| [54] | Castresana J (2000) Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Molecular biology and evolution 17: 540–552. doi: 10.1093/oxfordjournals.molbev.a026334
|
| [55] | Dereeper A, Guignon V, Blanc G, Audic S, Buffet S, et al. (2008) Phylogeny.fr: robust phylogenetic analysis for the non-specialist. Nucleic Acids Res 36: W465–469. doi: 10.1093/nar/gkn180
|
| [56] | Guindon S, Gascuel O (2003) A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Systematic biology 52: 696–704.
|
| [57] | Yang Z (2007) PAML 4: phylogenetic analysis by maximum likelihood. Mol Biol Evol 24: 1586–1591. doi: 10.1093/molbev/msm088
|
| [58] | Rosso MG, Li Y, Strizhov N, Reiss B, Dekker K, et al. (2003) An Arabidopsis thaliana T-DNA mutagenized population (GABI-Kat) for flanking sequence tag-based reverse genetics. Plant Mol Biol 53: 247–259. doi: 10.1023/b:plan.0000009297.37235.4a
|
| [59] | Alonso JM, Stepanova AN, Leisse TJ, Kim CJ, Chen H, et al. (2003) Genome-wide insertional mutagenesis of Arabidopsis thaliana. Science 301: 653–657. doi: 10.1126/science.1086391
|
| [60] | Murashige T, Skoog F (1962) A Revised Medium for Rapid Growth and Bio Assays with Tobacco Tissue Cultures. Physiologia plantarum 15: 473–497. doi: 10.1111/j.1399-3054.1962.tb08052.x
|
| [61] | Alonso-Blanco C, Aarts M, Bentsink L, Keurentjes J, Reymond M, et al. (2009) What has natural variation taught us about plant development, physiology, and adaptation? Plant Cell Online 21: 1877. doi: 10.1105/tpc.109.068114
|
| [62] | Shindo C, Bernasconi G, Hardtke CS (2008) Intraspecific competition reveals conditional fitness effects of single gene polymorphism at the Arabidopsis root growth regulator BRX. New Phytol 180: 71–80. doi: 10.1111/j.1469-8137.2008.02553.x
|
| [63] | Donohue K (2002) Germination timing influences natural selection on life-history characters in Arabidopsis thaliana. Ecology 83: 1006–1016. doi: 10.2307/3071909
|
| [64] | Pigliucci M, Schlichting CD (1996) Reaction norms of Arabidopsis IV. Relationships between plasticity and fitness. Heredity 76(Pt 5):427–436. doi: 10.1038/hdy.1996.65
|
| [65] | Shaw RG, Chang S-M (2006) Gene action of new mutations in Arabidopsis thaliana. Genetics 172: 1855–1865. doi: 10.1534/genetics.105.050971
|
| [66] | Mackinney G (1941) Absorption of light by chlorophyll solutions. J Biol Chem 140: 315–322.
|
