Skip to main content

A History of Genomic Structures: The Big Picture

  • Chapter
Plant Biology and Biotechnology
  • 4704 Accesses

Abstract

We present a comprehensive compilation of genomic structure evolution that should help the reader who is not familiar with genomics to understand the mechanisms that are shaping its structures over time. We believe that this understanding is essential to work with genomics in the sense that it should help to formulate productive hypothesis for new original works. We believe that the mechanism by which the extant genomic structures arose is more important than the shape of these structures since evolution is continuously at work. In addition, taking genomics under the evolution perspective gives the possibility to release a unified picture of its unlimited natural complexity to the reader without fair to be incomplete. It is amazing to realize how fast complex biological structures arose in the early time of Earth, and it has been our aim to try to give a constructive viewof the life journey to the reader.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 229.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 299.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 299.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  • Akashi M, Yoshikawa H (2013) Relevance of GC content to the conservation of DNA polymerase III/mismatch repair system in Gram-positive bacteria. Front Microbiol 4:266. doi:10.3389/fmicb.2013.00266

    PubMed Central  PubMed  Google Scholar 

  • Amborella Genome Project (2013) The Amborella genome and the evolution of flowering plants. Science 342. doi:10.1126/science.1241089

  • Amidi M, de Raad M, Crommelin DJ, Hennink WE, Mastrobattista E (2011) Antigen-expressing immunostimulatory liposomes as a genetically programmable synthetic vaccine. Syst Synth Biol 5:21–31

    PubMed Central  PubMed  Google Scholar 

  • Anantharaman V, Koonin EV, Aravind L (2002) Comparative genomics and evolution of proteins involved in RNA metabolism. Nucleic Acids Res 30:1427–1464

    CAS  PubMed Central  PubMed  Google Scholar 

  • Andras P, Andras C (2005) The origins of life – the ‘protein interaction world’ hypothesis: protein interactions were the first form of self-reproducing life and nucleic acids evolved later as memory molecules. Med Hypotheses 64(4):678–688

    CAS  PubMed  Google Scholar 

  • Arabidopsis Interactome Mapping Consortium (2011) Evidence for network evolution in an Arabidopsis interactome map. Science 333:601–606

    PubMed Central  Google Scholar 

  • Aravind L, Makarova KS, Koonin EV (2000) Survey and summary: holiday junction resolvases and related nucleases: identification of new families, phyletic distribution and evolutionary trajectories. Nucleic Acids Res 28:3417–3432

    CAS  PubMed Central  PubMed  Google Scholar 

  • Arhondakis S, Auletta F, Torelli G, D’Onofrio G (2004) Base composition and expression level of human genes. Gene 325:165–169

    CAS  PubMed  Google Scholar 

  • Arhondakis S, Auletta F, Bernardi G (2011) Isochores and the regulation of gene expression in the human genome. Genome Biol Evol 3:1080–1089

    CAS  PubMed Central  PubMed  Google Scholar 

  • Arnone MI, Davidson EH (1997) The hardwiring of development: organization and function of genomic regulatory systems. Development 124:1851–1864

    CAS  PubMed  Google Scholar 

  • Arora R, Agarwal P, Ray S, Singh AK, Singh VP, Tyagi AK, Kapoor S (2007) MADS-box gene family in rice: genome-wide identification, organization and expression profiling during reproductive development and stress. BMC Genomics 8:242

    PubMed Central  PubMed  Google Scholar 

  • Arumuganathan K, Earle ED (1991) Nuclear DNA content of some important plant species. Plant Mol Biol Report 9:208–218

    CAS  Google Scholar 

  • Avesson L (2011) Ancient roles of non-coding RNAs in eukaryotic evolution. PhD Thesis, Swedish University of Agricultural Sciences, Uppsala

    Google Scholar 

  • Banack SA, Metcalf JS, Jiang L, Craighead D, Ilag LL, Cox PA (2012) Cyanobacteria produce N-(2-aminoethyl)glycine, a backbone for peptide nucleic acids which may have been the first genetic molecules for life on earth. PLoS One 7(11):e49043

    CAS  PubMed Central  PubMed  Google Scholar 

  • Bartel DP, Szostak JW (1993) Isolation of new ribozymes from a large pool of random sequences. Science 261:1411–1418

    CAS  PubMed  Google Scholar 

  • Bartel DP, Unrau PJ (1999) Constructing an RNA world. Trends Cell Biol 9:M9–M13

    CAS  PubMed  Google Scholar 

  • Becker A, Saedler H, Theissen G (2003) Distinct MADS-box gene expression patterns in the reproductive cones of the gymnosperm Gnetum gnemon. Dev Genes Evol 213:567–572

    CAS  PubMed  Google Scholar 

  • Bell CD, Soltis DE, Soltis PS (2010) The age and diversification of the angiosperms re-revisited. Am J Bot 97(8):1296–1303

    PubMed  Google Scholar 

  • Bemer M, Heijmans K, Airoldi C, Davies B, Angenent GC (2010) An atlas of type I MADS box gene expression during female gametophyte and seed development in Arabidopsis. Plant Physiol 154:287–300

    CAS  PubMed Central  PubMed  Google Scholar 

  • Benner SA, Kim H-J, Yang Z (2012) Setting the stage: the history, chemistry, and geobiology behind RNA. Cold Spring Harb Perspect Biol 4:a003541

    PubMed Central  PubMed  Google Scholar 

  • Bennett MD (1996) The nucleotype, the natural karyotype and the ancestral genome. Symp Soc Exp Biol 50:45–52

    CAS  PubMed  Google Scholar 

  • Bennett MD, Smith JB (1976) Nuclear DNA amounts in angiosperms. Philos Trans R Soc Lond 274:227–274

    CAS  Google Scholar 

  • Bennetzen J (1996) The contributions of retroelements to plant genome organization, function and evolution. Trends Microbiol 4:347–353

    CAS  PubMed  Google Scholar 

  • Bernardi G (1989) The isochore organization of the human genome. Annu Rev Genet 23:637–661

    CAS  PubMed  Google Scholar 

  • Bernardi G (2000) Isochores and the evolutionary genomics of vertebrates. Gene 241:3–17

    CAS  PubMed  Google Scholar 

  • Bernardi G (2012) The genome: an isochore ensemble and its evolution. Ann N Y Acad Sci 1267:31–34

    CAS  PubMed  Google Scholar 

  • Bernhardt HS (2012) The RNA world hypothesis: the worst theory of the early evolution of life (except for all the others). Biol Direct 7:23

    CAS  PubMed Central  PubMed  Google Scholar 

  • Bernhardt HS, Tate WP (2010) The transition from noncoded to coded protein synthesis: did coding mRNAs arise from stability-enhancing binding partners to tRNA? Biol Direct 5:16

    PubMed Central  PubMed  Google Scholar 

  • Bétran E, Thornton K, Long M (2002) Retroposed new genes out of the X in Drosophila. Genome Res 12:1854–1859

    PubMed Central  PubMed  Google Scholar 

  • Brown KR, Jurisica I (2005) Online predicted human interaction database. Bioinformatics 21:2076–2082

    CAS  PubMed  Google Scholar 

  • Bucciarelli G, Di Filippo M, Costagliola D, Alvarez-Valin F, Bernardi G, Bernardi G (2009) Environmental genomics: a tale of two fishes. Mol Biol Evol 26(6):1235–1243

    CAS  PubMed  Google Scholar 

  • Burleigh JG, Barbazuk WB, Davis JM, Morse AM, Soltis PS (2012) Exploring diversification and genome size evolution in extant gymnosperms through phylogenetic synthesis. J Bot. doi:10.1155/2012/292857

    Google Scholar 

  • Butterfield NJ (2000) Bangiomorpha pubescens n. gen., n. sp.: implications for the evolution of sex, multicellularity, and the Mesoproterozoic/Neoproterozoic radiation of eukaryotes. Paleobiology 263:386–404

    Google Scholar 

  • Carels N (2005a) The genome organization of angiosperms. In: Pandalai SG (ed) Recent research developments in plant science. Research Signpost, Trivandrum, pp 129–194

    Google Scholar 

  • Carels N (2005b) The maize gene space is compositionally compartimentalized. FEBS Lett 579:3867–3871

    CAS  PubMed  Google Scholar 

  • Carels N, Bernardi G (2000a) The compositional organization and the expression of the Arabidopsis genome. FEBS Lett 472:302–306

    CAS  PubMed  Google Scholar 

  • Carels N, Bernardi G (2000b) Two classes of genes in plants. Genetics 154:1819–1825

    CAS  PubMed Central  PubMed  Google Scholar 

  • Carels N, Frias D (2009) Classifying coding DNA with nucleotide statistics. Bioinforma Biol Insights 3:141–154

    CAS  Google Scholar 

  • Carels N, Frias DA (2013) Statistical method without training step for the classification of coding frame in transcriptome sequences. Bioinforma Biol Insights 7:35–54

    CAS  Google Scholar 

  • Carels N, Ponce de Leon M (2015) An interpretation of the ancestral codon from Miller’s amino acids and nucleotide correlations in modern coding sequences. Bioinf Biol Insights 9:37–47

    Google Scholar 

  • Carels N, Hatey P, Jabbari K, Bernardi G (1998) Compositional properties of homologous coding sequences from plants. J Mol Evol 46:45–53

    CAS  PubMed  Google Scholar 

  • Carels N, Vidal R, Frias D (2009) Universal features for the classification of coding and non-coding DNA sequences. Bioinforma Biol Insights 3:1–13

    Google Scholar 

  • Carthew RW, Sontheimer EJ (2009) Origins and mechanisms of miRNAs and siRNAs. Cell 136:642–655

    CAS  PubMed Central  PubMed  Google Scholar 

  • Cavalier-Smith T (2001) Obcells as proto-organisms: membrane heredity, lithophosphorylation, and the origins of the genetic code, the first cells, and photosynthesis. J Mol Evol 53:555–595

    CAS  PubMed  Google Scholar 

  • Cavalier-Smith T (2002) The phagotrophic origin of eukaryotes and phylogenetic classification of protozoa. Int J Syst Evol Microbiol 52:297–354

    CAS  PubMed  Google Scholar 

  • Cavalier-Smith T (2004) Only six kingdoms of life. Proc Biol Sci 271:1251–1262

    CAS  PubMed Central  PubMed  Google Scholar 

  • Cech TR (2012) The RNA worlds in context. Cold Spring Harb Perspect Biol 4:a006742

    PubMed Central  PubMed  Google Scholar 

  • Chauhan RS, Sood (2013) A comparative genomics in euphorbiaceae. In: Bahadur B, Sujatha M, Carels N (eds) Jatropha, challenges for a new energy crop, vol 2, Genetic Improvement and Biotechnology (Chap. 18). Springer, New York, pp 351–374

    Google Scholar 

  • Chen G, Courey AJ (2000) Groucho/TLE family proteins and transcriptional repression. Gene 249:1–16

    CAS  PubMed  Google Scholar 

  • Cheng LKL, Unrau PJ (2010) Closing the circle: replicating RNA with RNA. Cold Spring Harb Perspect Biol 2:a002204

    CAS  PubMed Central  PubMed  Google Scholar 

  • Cheng LKL, Unrau PJ (2012) Closing the circle: replicating RNA with RNA. Cold Spring Harb Perspect Biol 4:a003566

    Google Scholar 

  • Clarke J, Wu H-C, Jayasinghe L, Patel A, Reid S, Bayley H (2009) Continuous base identification for single-molecule nanopore DNA sequencing. Nat Nanotechnol 4:265–270

    CAS  PubMed  Google Scholar 

  • Clay O, Carels N, Douady C, Macaya G, Bernardi G (2001) Compositional heterogeneity within and among isochores in mammalian genomes I. CsCl and sequence analyses. Gene 276:15–24

    CAS  PubMed  Google Scholar 

  • Clay O, Douady CJ, Carels N, Hughes S, Bucciarelli G, Bernardi G (2003) Using analytical ultracentrifugation to study compositional variation in vertebrate genomes. Eur Biophys J 32:418–426

    CAS  PubMed  Google Scholar 

  • Costantini M, Bernardi G (2008) Correlations between coding and contiguous non-coding sequences in isochore families from vertebrate genomes. Gene 410:241–248

    CAS  PubMed  Google Scholar 

  • Costantini M, Clay O, Auletta F, Bernardi G (2006) An isochore map of human chromosomes. Genome Res 16:536–541

    CAS  PubMed Central  PubMed  Google Scholar 

  • Costantini M, Di Filippo M, Auletta F, Bernardi G (2007a) Isochore pattern and gene distribution in the chicken genome. Gene 400:9–15

    CAS  PubMed  Google Scholar 

  • Costantini M, Clay O, Federico C, Saccone S, Auletta F, Bernardi G (2007b) Human chromosomal bands: nested structure, high-definition map and molecular basis. Chromosoma 116:29–40

    CAS  PubMed  Google Scholar 

  • Costantini M, Cammarano R, Bernardi G (2009) The evolution of isochore patterns in vertebrate genomes. BMC Genomics 10:146. doi:10.1186/1471-2164-10-146

    PubMed Central  PubMed  Google Scholar 

  • Costantini M, Auletta F, Bernardi G (2012) The distributions of “new” and “old” Alu sequences in the human genome: the solution of a “mystery”. Mol Biol Evol 29:421–427

    CAS  PubMed  Google Scholar 

  • Costantini M, Alvarez-Valin F, Costantini S, Cammarano R, Bernardi G (2013) Compositional patterns in the genomes of unicellular eukaryotes. BMC Genomics 14:755

    CAS  PubMed Central  PubMed  Google Scholar 

  • Cruveiller S, Jabbari K, Clay O, Bernardi G (2004) Compositional gene landscapes in vertebrates. Genome Res 14:886–892

    CAS  PubMed Central  PubMed  Google Scholar 

  • D’Onofrio G, Jabbari K, Musto H, Bernardi G (1999) The correlation of protein hydropathy with the base composition of coding sequences. Gene 238:3–14

    PubMed  Google Scholar 

  • Davies PCW, Benner SA, Cleland CE, Lineweaver CH, McKay CP, Wolfe-Simon F (2009) Signatures of a shadow biosphere. Astrobiology 9:241–249

    PubMed  Google Scholar 

  • Deragon JM, Landry BS, Pelissier T, Tutois S, Tourmente S, Picard G (1994) An analysis of retroposition in plants based on a family of SINEs from Brassica napus. J Mol Evol 39:378–386

    CAS  PubMed  Google Scholar 

  • Di Giulio M (1992) On the origin of the transfer RNA molecule. J Theor Biol 159:199–214

    PubMed  Google Scholar 

  • Di Giulio M (2001) The universal ancestor was a thermophile or a hyperthermophile. Gene 281:11–17

    PubMed  Google Scholar 

  • Di Giulio M (2006) The non-monophyletic origin of the tRNA molecule and the origin of genes only after the evolutionary stage of the Last Universal Common Ancestor (LUCA). J Theor Biol 240:343–352

    PubMed  Google Scholar 

  • Di Giulio M (2008) The origin of genes could be polyphyletic. Gene 426:39–46

    PubMed  Google Scholar 

  • Di Ruggiero J, Robb FT (2004) Early evolution of DNA repair mechanisms. In: de Pouplana LR (ed) The genetic code and the origin of life (Ch. 14). Kluwer Academic/Plenum Publishers, New York, USA, pp 169–182

    Google Scholar 

  • Dolan L (2009) Body building on land—morphological evolution of land plants. Curr Opin Plant Biol 12:4–8

    CAS  PubMed  Google Scholar 

  • Duret L, Mouchiroud D, Gautier C (1995) Statistical analysis of vertebrate sequences reveals that long genes are scarce in GC-rich isochores. J Mol Evol 40:308–317

    CAS  PubMed  Google Scholar 

  • Dyall SD, Brown MT, Johnson PJ (2004) Ancient invasions: from endosymbionts to organelles. Science 304:253–257

    CAS  PubMed  Google Scholar 

  • Eid J, Fehr A, Gray J, Luong K, Lyle J, Otto G et al (2009) Real-time DNA sequencing from single polymerase molecules. Science 323:133–138

    CAS  PubMed  Google Scholar 

  • Eigen M, Schuster P (1977) The hypercycle. A principle of natural self-organisation. Part A: emergence of the hypercycle. Naturwissenschaften 64:541–565

    CAS  PubMed  Google Scholar 

  • Eigen M, Schuster P (1978a) The hypercycle. A principle of natural self-organisation. Part B: the abstract hypercycle. Naturwissenschaften 65:7–41

    Google Scholar 

  • Eigen M, Schuster P (1978b) The hypercycle. A principle of natural self-organisation. Part C: the realistic hypercycle. Naturwissenschaften 65:341–369

    CAS  Google Scholar 

  • Erayman M, Sandhu D, Sidhu D, Dilbirligi M, Baenziger PS, Gill KS (2004) Demarcating the gene-rich regions of the wheat genome. Nucleic Acids Res 32:3546–3565

    CAS  PubMed Central  PubMed  Google Scholar 

  • Eschenmoser A (2004) The TNA-family of nucleic acid systems: properties and prospects. Orig Life Evol Biosph 34:277–306

    CAS  PubMed  Google Scholar 

  • Farnell DA (2011) Nucleotide excision repair in the three domains of life. West Undergr Res J Health Nat Sci 2:1–6. doi:10.5206/wurjhns. 2010-11.1

    Google Scholar 

  • Fechheimer NS, Isakova GK, Belyaev DK (1983) Mechanisms involved in the spontaneous occurrence of diploid-triploid chimerism in the mink (Mustela vison) and chicken (Gallus domesticus). Cytogenet Cell Genet 35:238–243

    CAS  PubMed  Google Scholar 

  • Filée J, Forterre P, Sen-Lin T, Laurent J (2002) Evolution of DNA polymerase families: evidences for multiple gene exchange between cellular and viral proteins. J Mol Evol 54:763–773

    PubMed  Google Scholar 

  • Flowers JM, Molina J, Rubinstein S, Huang P, Schaal BA, Purugganan MD (2012) Natural selection in gene-dense regions shapes the genomic pattern of polymorphism in wild and domesticated rice. Mol Biol Evol 29(2):675–687

    CAS  PubMed  Google Scholar 

  • Forterre P (2001) Genomics and early cellular evolution. The origin of the DNA world. C R Acad Sci Paris Sci de la vie/Life Sci 324:1067–1076

    CAS  Google Scholar 

  • Forterre P (2005) The two ages of the RNA world, and the transition to the DNA world: a story of viruses and cells. Biochimie 87:793–803

    CAS  PubMed  Google Scholar 

  • Forterre P (2006) Three RNA cells for ribosomal lineages and three DNA viruses to replicate their genomes: a hypothesis for the origin of cellular domain. Proc Natl Acad Sci U S A 103:3669–3674

    CAS  PubMed Central  PubMed  Google Scholar 

  • Friedman WE, Moore RC, Purugganan MD (2004) The evolution of plant development. Am J Bot 91(10):1726–1741

    PubMed  Google Scholar 

  • Friesen N, Brandes A, Heslop-Harrison JS (2001) Diversity, origin, and distribution of retrotransposons (gypsy and copia) in conifers. Mol Biol Evol 18:1176–1188

    CAS  PubMed  Google Scholar 

  • Fuerst JA, Sagulenko E (2013) Nested bacterial boxes: nuclear and other intracellular compartments in planctomycetes. J Mol Microbiol Biotechnol 23:95–103

    CAS  PubMed  Google Scholar 

  • Gabriel M (1960) Primitive genetic mechanisms and the origin of chromosomes. Am Nat 94:257–269

    Google Scholar 

  • Gaeta RT, Masonbrink RE, Krishnaswamy L, Zhao C, Birchler JA (2012) Synthetic chromosome platforms in plants. Annu Rev Plant Biol 63:307–330

    CAS  PubMed  Google Scholar 

  • Gale MD, Devos KM (1998) Plant comparative genetics after 10 years. Science 282:656–659

    CAS  PubMed  Google Scholar 

  • Gallardo MH, Kausel G, Jiménez A, Bacquet C, González C, Figueroa J, Köhler N, Ojeda R (2004) Whole-genome duplications in South American desert rodents (Octodontidae). Biol J Linn Soc 82:443–451

    Google Scholar 

  • Garcia-Fernàndez J (2005) The genesis and evolution of homeobox gene clusters. Nat Rev Genet 6:881–892

    PubMed  Google Scholar 

  • Geisler S, Lojek L, Khalil AM, Baker KE, Coller J (2012) Decapping of long noncoding RNAs regulates inducible genes. Mol Cell 45:279–291

    CAS  PubMed Central  PubMed  Google Scholar 

  • Gerstein MB, Bruce C, Rozowsky JS, Zheng D, Du J, Korbel JO, Emanuelsson O, Zhang ZD, Weissman S, Snyder M (2007) What is a gene, post-ENCODE? History and updated definition. Genome Res 17:669–681

    CAS  PubMed  Google Scholar 

  • Geuten K, Coenen H (2013) Heterochronic genes in plant evolution and development. Front Plant Sci 4:381. doi:10.3389/fpls.2013.00381

    PubMed Central  PubMed  Google Scholar 

  • Gibson DG, Glass JI, Lartigue C, Noskov VN, Chuang RY et al (2010) Creation of a bacterial cell controlled by a chemically synthesized genome. Science 329:38–39

    Google Scholar 

  • Gilbert W (1986) Origin of life: the RNA world. Nature 319:618

    Google Scholar 

  • Gilbert W, de Souza SJ (1999) Introns and the RNA world. In: The RNA world (Ch. 9), 2nd edn. Cold Spring Harbor Laboratory Press, pp 221–231. 0-87969-561-7/99

    Google Scholar 

  • Glaser R, Hodgen B, Farrelly D, McKee E (2007) Adenine synthesis in interstellar space: mechanisms of prebiotic pyrimidine-ring formation of monocyclic HCN-pentamers. Astrobiology 7(3):455–470

    CAS  PubMed  Google Scholar 

  • Gold L, Janjic N, Jarvis T, Schneider D, Walker JJ, Wilcox SK, Zichi D (2012) Aptamers and the RNA world, past and present. Cold Spring Harb Perspect Biol 4:a006742

    Google Scholar 

  • Goodyer CG, Zogopolos G, Schwartzbauer G, Zheng H, Hendy GN, Menon RK (2001) Organization and evolution of the human growth hormone receptor 5′-flanking region. Endocrinology 142:1923–1934

    CAS  PubMed  Google Scholar 

  • Graham LE, Cook ME, Busse JS (2000) The origin of plants: body plan changes contributing to a major evolutionary radiation. Proc Natl Acad Sci U S A 97(9):4535–4540

    CAS  PubMed Central  PubMed  Google Scholar 

  • Gregory TR, Mable BK (2005) Polyploidy in animals. In: Gregory TR (ed) The evolution of the genome (Chap. 8). Elsevier, San Diego, pp 427–517

    Google Scholar 

  • Gronostajski RM, Guaneri J, Lee DH, Gallo SM (2011) The NFI-Regulome database: a tool for annotation and analysis of control regions of genes regulated by nuclear factor I transcription factors. Int J Clin Bioinforma 1:4

    CAS  Google Scholar 

  • Grosberg RK, Strathmann RR (2007) The evolution of multicellularity: a minor major transition? Annu Rev Ecol Evol Syst 38:621–654

    Google Scholar 

  • Hanczyc MM, Szostak JW (2004) Replicating vesicles as models of primitive cell growth and division. Curr Opin Chem Biol 8:660–664

    CAS  PubMed  Google Scholar 

  • Henikoff S, Ahmad K, Malik HS (2001) The centromere paradox: stable inheritance with rapidly evolving DNA. Science 293:1098–1102

    CAS  PubMed  Google Scholar 

  • Hildebrand F, Meyer A, Eyre-Walker A (2010) Evidence of selection upon genomic GC-content in bacteria. PLoS Genet 6:e1001107

    PubMed Central  PubMed  Google Scholar 

  • Horst JP, Wu TH, Marinus MG (1999) Escherichia coli mutator genes. Trends Microbiol 7:29–36

    CAS  PubMed  Google Scholar 

  • Hosoda K, Sunami T, Kazuta Y, Matsuura T, Suzuki H, Yomo T (2008) Quantitative study of the structure of multilamellar giant liposomes as a container of protein synthesis reaction. Langmuir 24:13540–13548

    CAS  PubMed  Google Scholar 

  • Huang Q, Li W, Fan R, Chang Y (2014) New MADS-box gene in fern: cloning and expression analysis of DfMADS1 from dryopteris fragrans. PLoS One 9(1):e86349

    PubMed Central  PubMed  Google Scholar 

  • Ikehara K (2009) Pseudo-replication of [GADV]-proteins and origin of life. Int J Mol Sci 10:1525–1537. doi:10.3390/ijms10041525

    CAS  PubMed Central  PubMed  Google Scholar 

  • Illergård K, Ardell DH, Elofsson A (2009) Structure is three to ten times more conserved than sequence – a study of structural response in protein cores. Proteins 77:499–508

    PubMed  Google Scholar 

  • Imai HT, Maruyama T, Gojobori T, Inoue Y, Crozier RH (1986) Theoretical bases for karyotype evolution. 1. The minimum-interaction hypothesis. Am Nat 128:900–920

    Google Scholar 

  • Jensen NM, Dalsgaard T, Jakobsen M, Nielsen RR, Sørensen CB, Bolund L, Jensen TG (2011) An update on targeted gene repair in mammalian cells: methods and mechanisms. J Biomed Sci 18:10

    CAS  PubMed Central  PubMed  Google Scholar 

  • Jiang N, Feschotte C, Zhang X, Wessler SR (2004) Using rice to understand the origin and amplification of miniature inverted repeat transposable elements MITEs). Curr Opin Plant Biol 7:115–119

    CAS  PubMed  Google Scholar 

  • Jiao Y et al (2011) Ancestral polyploidy in seed plants and angiosperms. Nature 473:97–102

    CAS  PubMed  Google Scholar 

  • Jin J, Liu J, Wang H, Wong L, Chua NH (2013) PLncDB: plant long non-coding RNA database. Bioinformatics 29(8):1068–1071

    CAS  PubMed Central  PubMed  Google Scholar 

  • Kanehisa M, Goto S (2000) KEGG: Kyoto encyclopedia of genes and genomes. Nucleic Acids Res 28(1):27–30

    CAS  PubMed Central  PubMed  Google Scholar 

  • Kater MM, Dreni L, Colombo L (2006) Functional conservation of MADS-box factors controlling floral organ identity in rice and Arabidopsis. J Exp Bot 57:3433–3444

    CAS  PubMed  Google Scholar 

  • Khalil AS, Collins JJ (2010) Synthetic biology: applications come of age. Nat Rev Genet 11:367–379

    CAS  PubMed Central  PubMed  Google Scholar 

  • Kidwell MG (2005) Transposable elements. In: Gregory TR (ed) The evolution of the genome (Ch.3). Elsevier, San Diego, pp 165–221

    Google Scholar 

  • Kim KM, Caetano-Anollés G (2011) The proteomic complexity and rise of the primordial ancestor of diversified life. BMC Evol Biol 11:140

    CAS  PubMed Central  PubMed  Google Scholar 

  • Knight RD, Landweber LF (1998) Rhyme or reason: RNA-arginine interactions and the genetic code. Chem Biol 5:R215–R220

    CAS  PubMed  Google Scholar 

  • Köhler C, Weinhofer-Molisch I (2010) Mechanisms and evolution of genomic imprinting in plants. Heredity 105:57–63

    PubMed  Google Scholar 

  • Koskela M, Annila A (2012) Looking for the Last Universal Common Ancestor (LUCA). Gene 3:81–87. doi:10.3390/genes3010081

    CAS  Google Scholar 

  • Kovach A, Wegrzyn JL, Parra G, Holt C, Bruening GE, Loopstra 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

    PubMed Central  PubMed  Google Scholar 

  • Kurihara K, Tamura M, K-i S, Toyota T, Suzuki K, Sugawara T (2011) Self-reproduction of supramolecular giant vesicles combined with the amplification of encapsulated DNA. Nat Chem 3:775–781

    CAS  PubMed  Google Scholar 

  • Kuruma Y, Stano P, Ueda T, Luisi PL (2009) A synthetic biology approach to the construction of membrane proteins in semisynthetic minimal cells. Biochim Biophys Acta 1788:567–574

    CAS  PubMed  Google Scholar 

  • Langdale JA, Harrison CJ (2008) Developmental transition during the evolution of plant form. In: Minelli A, Fusco G (eds) Evolving pathways key themes in evolutionary developmental biology (Chap. 16). Cambridge University Press, Cambridge, UK, pp 299–316

    Google Scholar 

  • Lau MW, Cadieux KE, Unrau PJ (2004) Isolation of fast purine nucleotide synthase ribozymes. J Am Chem Soc 126:15686–15693

    CAS  PubMed  Google Scholar 

  • Lee TI, Young RA (2000) Transcription of eukaryotic protein-coding genes. Annu Rev Genet 34:77–137

    CAS  PubMed  Google Scholar 

  • Lee TI, Rinaldi NJ, Robert F et al (2002) Transcriptional regulatory networks in Saccharomyces cerevisiae. Science 298:799–804

    CAS  PubMed  Google Scholar 

  • Leitch IJ, Chase MW, Bennett MD (1998) Phylogenetic analysis of DNA C-values provides evidence for a small ancestral genome size in flowering plants. Ann Bot 82(Suppl A):85–94

    CAS  Google Scholar 

  • Lindsay MR, Webb RI, Strous M, Jetten MS, Butler MK, Forde RJ, Fuerst JA (2001) Cell compartmentalisation in planctomycetes: novel types of structural organisation for the bacterial cell. Arch Microbiol 175:413–429

    CAS  PubMed  Google Scholar 

  • Liu Y, Cui S, Wu F, Yan S, Lin X, Du X, Chong K, Schilling S, Theißen G, Meng Z (2013) Functional conservation of MIKC*-type MADS box genes in Arabidopsis and rice pollen maturation. Plant Cell. doi:10.1105/tpc.113.110049

    Google Scholar 

  • Luisi PL, Allegretti M, Pereira de Souza T, Steiniger F, Fahr A, Stano P (2010) Spontaneous protein crowding in liposomes: a new vista for the origin of cellular metabolism. Chembiochem 11:1989–1992

    CAS  PubMed  Google Scholar 

  • Lukas A et al (2009) A snapshot of the emerging tomato genome sequence. Plant Genome 2(1):78–92

    Google Scholar 

  • Makarova KS, Wolf YI, van der Oost J, Koonin EV (2009) Prokaryotic homologs of Argonaute proteins are predicted to function as key components of a novel system of defense against mobile genetic elements. Biol Direct 4:29

    PubMed Central  PubMed  Google Scholar 

  • Maltsev N, Glass E, Sulakhe D, Rodriguez A, Syed MH, Bompada T, Zhang Y, D’Souza M (2006) PUMA2–grid-based high-throughput analysis of genomes and metabolic pathways. Nucleic Acids Res 34(Database issue):D369–D372

    CAS  PubMed Central  PubMed  Google Scholar 

  • Martienssen RA, Rabinowicz PD, O’Shaughnessy A, McCombie WR (2004) Sequencing the maize genome. Curr Opin Plant Biol 7:102–107

    CAS  PubMed  Google Scholar 

  • Martin W, Russell MJ (2003) On the origins of cells: a hypothesis for the evolutionary transitions from abiotic geochemistry to chemoautotrophic prokaryotes, and from prokaryotes to nucleated cells. Philos Trans R Soc Lond B Biol Sci 358:59–85

    CAS  PubMed Central  PubMed  Google Scholar 

  • Matassi G, Melis R, Macaya G, Bernardi G (1991) Compositional bimodality of the nuclear genome of tobacco. Nucleic Acids Res 19:5561–5567

    CAS  PubMed Central  PubMed  Google Scholar 

  • Mathews DH, Moss WN, Turner DH (2010) Folding and finding RNA secondary structure. Cold Spring Harb Perspect Biol. doi:10.1101/cshperspect.a003665

    PubMed Central  PubMed  Google Scholar 

  • Mazurie A, Bonchev D, Schwikowski B, Buck GA (2010) Evolution of metabolic network organization. BMC Syst Biol 4:59

    PubMed Central  PubMed  Google Scholar 

  • McCutcheon JP, Moran NA (2010) Functional convergence in reduced genomes of bacterial symbionts spanning 200 My of evolution. Genome Biol Evol 2:708–718

    PubMed Central  PubMed  Google Scholar 

  • McGlynn SE, Beard TE, Broderick JB, Peters JW (2010) Life’s origins: potential for radical mediated cyanide production on the early earth. J Cosmol 10:3315–3324

    Google Scholar 

  • Meyers BC, Tingey SV, Morgante M (2001) Abundance, distribution, and transcriptional activity of repetitive elements in the maize genome. Genome Res 11:1660–1676

    CAS  PubMed Central  PubMed  Google Scholar 

  • Michael TP, Jackson S (2013) The first 50 plant genomes. Plant Genome 6(2):1–7

    Google Scholar 

  • Miller SL (1987) Which organic compounds could have occurred on the prebiotic earth? Cold Spring Harb Symp Quant Biol 52:17–27

    CAS  PubMed  Google Scholar 

  • Miller DF, Rogers BT, Kalkbrenner A, Hamilton B, Holtzman SL, Kaufman T (2001) Cross-regulation of Hox genes in the Drosophila melanogaster embryo. Mech Dev 102:3–16

    CAS  PubMed  Google Scholar 

  • Mithani A, Preston GM, Hein J (2009) A stochastic model for the evolution of metabolic networks with neighbor dependence. Bioinformatics 25:1528–1535

    CAS  PubMed  Google Scholar 

  • Mithani A, Preston GM, Hein J (2010) Bayesian approach to the evolution of metabolic networks on a phylogeny. PLoS Comput Biol 6:e1000868

    PubMed Central  PubMed  Google Scholar 

  • Molnar A, Schwach F, Studholme DJ, Thuenemann EC, Baulcombe DC (2007) miRNAs control gene expression in the single-cell alga Chlamydomonas reinhardtii. Nature 447:1126–1129

    CAS  PubMed  Google Scholar 

  • Montavon T, Duboule D (2013) Chromatin organization and global regulation of Hox gene clusters. Philos Trans R Soc B 368:1–8, 20120367

    Google Scholar 

  • Moore PB, Steitz TA (2002) The involvement of RNA in ribosome function. Nature 418:229–235

    CAS  PubMed  Google Scholar 

  • Motta LS, Ramos IB, Gomes FM, de Souza W, Champagne DE, Santiago MF, Docampo R, Miranda K, Machado EA (2009) Proton-pyrophosphatase and polyphosphate in acidocalcisome-like vesicles from oocytes and eggs of Periplaneta americana. Insect Mol Biol 39:198–206

    CAS  Google Scholar 

  • Mukherjee K, Brocchieri L, Bürglin TR (2009) A comprehensive classification and evolutionary analysis of plant homeobox genes. Mol Biol Evol 26(12):2775–2794

    CAS  PubMed Central  PubMed  Google Scholar 

  • Murray AW, Szostak JW (1983) Construction of artificial chromosomes in yeast. Nature 305:189–193

    CAS  PubMed  Google Scholar 

  • Murtas G (2009) Artificial assembly of a minimal cell. Mol Biosyst 5:1292–1297

    CAS  PubMed  Google Scholar 

  • Nam K, Ellegren H (2012) Recombination drives vertebrate genome contraction. PLoS Genet 8(5):e1002680

    CAS  PubMed Central  PubMed  Google Scholar 

  • Nandagopal N, Elowitz MB (2011) Synthetic biology: integrated gene circuits. Science 333:1244–1248

    CAS  PubMed Central  PubMed  Google Scholar 

  • Nobrega MA, Ovcharenko I, Afzal V, Rubin EM (2003) Scanning human gene deserts for long-range enhancers. Science 302:413

    CAS  PubMed  Google Scholar 

  • Noireaux V, Libchaber A (2004) A vesicle bioreactor as a step toward an artificial cell assembly. Proc Natl Acad Sci U S A 101:17669–17674

    CAS  PubMed Central  PubMed  Google Scholar 

  • Noireaux V, Maeda YT, Libchaber A (2011) Development of an artificial cell, from self-organization to computation and self-reproduction. Proc Natl Acad Sci U S A 108:3473–3480

    CAS  PubMed Central  PubMed  Google Scholar 

  • O’Connor M, Peifer M, Bender W (1989) Construction of large DNA segments in Escherichia coli. Science 244:1307–1312

    PubMed  Google Scholar 

  • Oba T, Fukushima J, Maruyama M, Iwamoto R, Ikehara K (2005) Catalytic activities of [GADV]-peptides. Orig Life Evol Biosph 34:447–460

    Google Scholar 

  • Ohri D, Khoshoo TN (1986) Genome size in gymnosperms. Plant Syst Evol 153:119–132

    Google Scholar 

  • Orgel LE (2000) Self-organizing biochemical cycles. Proc Natl Acad Sci U S A 97:12503–12507

    CAS  PubMed Central  PubMed  Google Scholar 

  • Paces J, Zika R, Paces V, Pavlicek A, Clay O, Bernardi G (2004) Representing GC variation along eukaryotic chromosomes. Gene 333:135–141

    CAS  PubMed  Google Scholar 

  • Patel M, Jiang Q, Woodgate R, Cox MM, Goodman MF (2010) A new model for SOS-induced mutagenesis: how RecA protein activates DNA polymerase V. Crit Rev Biochem Mol Biol 45(3):171–184

    CAS  PubMed Central  PubMed  Google Scholar 

  • Paterson AH et al (1996) Toward a unified genetic map of higher plants, transcending the monocot-dicot divergence. Nat Genet 14:380–382

    CAS  PubMed  Google Scholar 

  • Pavlicek A, Jabbari K, Paces J, Paces V, Hejnar J, Bernardi G (2001) Similar integration but different stability of Alus and LINEs in the human genome. Gene 276:39–45

    CAS  PubMed  Google Scholar 

  • Pavlicek A, Paces J, Clay O, Bernardi G (2002) A compact view of isochores in the draft human genome sequence. FEBS Lett 511(1–3):165–169

    CAS  PubMed  Google Scholar 

  • Pélissier T, Bousquet-Antonelli C, Lavie L, Deragon J-M (2004) Synthesis and processing of tRNA-related SINE transcripts in Arabidopsis thaliana. Nucleic Acids Res 32:3957–3966

    PubMed Central  PubMed  Google Scholar 

  • Pereira de Souza T, Stano P, Luisi PL (2009) The minimal size of liposome-based model cells brings about a remarkably enhanced entrapment and protein synthesis. Chembiochem 10:1056–1063

    CAS  PubMed  Google Scholar 

  • Peterson-Burch BD, Voytas DF (2002) Genes of the Pseudoviridae (Ty1/copia Retrotransposons). Mol Biol Evol 19:1832–1845

    CAS  PubMed  Google Scholar 

  • Pires-daSilva A, Sommer RJ (2003) The evolution of signaling pathways in animal development. Nat Rev Genet 4:39–49

    CAS  PubMed  Google Scholar 

  • Ponce de Leon M, de Miranda AB, Alvarez-Valin F, Carels N (2014) The purine bias of coding sequences is encoded by physicochemical constraints on proteins. Bioinforma Biol Insights 8:93–108

    Google Scholar 

  • Powner MW, Gerland B, Sutherland JD (2009) Synthesis of activated pyrimidine ribonucleotides in prebiotically plausible conditions. Nature 459:239–242

    CAS  PubMed  Google Scholar 

  • Putnam NH, Srivastava M, Hellsten U, Dirks B, Chapman J, Salamov A, Terry A, Shapiro H, Lindquist E, Kapitonov VV, Jurka J, Genikhovich G, Grigoriev IV, Lucas SM, Steele RE, Finnerty JR, Technau U, Martindale MQ, Rokhsar DS (2007) Sea Anemone genome reveals ancestral Eumetazoan gene repertoire and genomic organization. Science 317:86–94

    CAS  PubMed  Google Scholar 

  • Raoult D, Audic S, Robert C, Abergel C, Renesto P, Ogata H, La Scola B, Suzan M, Claverie JM (2004) The 1.2-megabase genome sequence of Mimivirus. Science 306:1344–1350

    CAS  PubMed  Google Scholar 

  • Ricardo A, Carrigan MA, Olcott AN, Benner SA (2004) Borate minerals stabilize ribose. Science 303:196

    CAS  PubMed  Google Scholar 

  • Ritchie DB, Schellenberg MJ, MacMillan AM (2009) Spliceosome structure: piece by piece. Biochim Biophys Acta 1789:624–633

    CAS  PubMed  Google Scholar 

  • Rodríguez-Trelles F, Tarrío R, Ayala FJ (2006) Origins and evolution of spliceosomal introns. Annu Rev Genet 40:47–76

    PubMed  Google Scholar 

  • Rogozin IB, Carmel L, Csuros M, Koonin EV (2012) Origin and evolution of spliceosomal introns. Biol Direct 7:11

    CAS  PubMed Central  PubMed  Google Scholar 

  • Roy D, Najafian K, von Ragué Schleyer P (2007) Chemical evolution: the mechanism of the formation of adenine under prebiotic conditions. Proc Natl Acad Sci USA 104:17272–17277

    CAS  PubMed Central  PubMed  Google Scholar 

  • Ruder WC, Lu T, Collins JJ (2011) Synthetic biology moving into the clinic. Science 333:1248–1252

    CAS  PubMed  Google Scholar 

  • Rynditch AV, Zoubak S, Tsyb L, Tryapitsina-Guley N, Bernardi G (1998) The regional integration of retroviral sequences into the mosaic genomes of mammals. Gene 222:1–16

    CAS  PubMed  Google Scholar 

  • Saccone S, Federico C, Bernardi G (2002) Localization of the gene-richest and the gene-poorest isochores in the interphase nuclei of mammals and birds. Gene 300:169–178

    CAS  PubMed  Google Scholar 

  • Sagan L (1967) On the origin of mitosing cells. J Theor Biol 14:225–274

    CAS  Google Scholar 

  • Sandhu D, Gill KS (2002) Gene containing regions of wheat and the other grass genomes. Plant Physiol 128:803–811

    CAS  PubMed Central  PubMed  Google Scholar 

  • Sankoff D, Zheng C, Zhu Q (2010) The collapse of gene complement following whole genome duplication. BMC Genomics 11:313

    PubMed Central  PubMed  Google Scholar 

  • SanMiguel P, Tikhonov A, Jin Y-K, Motchoulskaia N, Zakharov D, Melake-Berhan A, Springer PS, Edwards KJ, Lee M, Avramova Z, Bennetzen J (1996) Nested retrotransposons in the intergenic regions of the maize genome. Sciences 274:765–768

    CAS  Google Scholar 

  • Santos H, da Costa MS (2002) Compatible solutes of organisms that live in hot saline environments. Environ Microbiol 4:501–509

    CAS  PubMed  Google Scholar 

  • Schmidt R (2002) Plant genome evolution: lessons from comparative genomics at the DNA level. Plant Mol Biol 48:21–37

    CAS  PubMed  Google Scholar 

  • Schopf JW (1993) Microfossils of the early archean apex chert: new evidence of the antiquity of life. Science 260:640–646

    CAS  PubMed  Google Scholar 

  • Schubert I (2007) Chromosome evolution. Curr Opin Plant Biol 10:109–115

    CAS  PubMed  Google Scholar 

  • Schubert I, Pecinka A, Meister A, Schubert V, Klatte M, Jovtchev G (2004) DNA damage processing and aberration formation in plants. Cytogenet Genome Res 104:104–108

    CAS  PubMed  Google Scholar 

  • Schuster P (1996) How does complexity arise in evolution: nature’s recipe for mastering scarcity, abundance, and unpredictability. doi:10.1002/(SICI)1099-0526(199609/10)2:1<22::AID-CPLX6>3.0.CO;2-H

  • Schwartz JH (1999) Homeobox genes, fossils, and the origin of species. Anat Rec (N Anat) 257:15–31

    CAS  Google Scholar 

  • Serres-Giardi L, Belkhir K, David J, Glémin S (2012) Patterns and evolution of nucleotide landscapes in seed plants. Plant Cell 24:1379–1397

    CAS  PubMed Central  PubMed  Google Scholar 

  • Seufferheld MJ, Kim KM, Whitfield J, Valerio A, Caetano-Anollés G (2011) Evolution of vacuolar proton pyrophosphatase domains and volutin granules: clues into the early evolutionary origin of the acidocalcisome. Biol Direct 6:50

    CAS  PubMed Central  PubMed  Google Scholar 

  • Shimizu Y, Inoue A, Tomari Y, Suzuki T, Yokogawa T, Nishikawa K, Ueda T (2001) Cell-free translation reconstituted with purified components. Nat Biotechnol 19:751–755

    CAS  PubMed  Google Scholar 

  • Soltis DE, Albert VA, Leebens-Mack J, Bell CD, Paterson AH, Zheng C, Sankoff D, dePamphilis CW, Wall PK, Soltis PS (2009) Polyploidy and angiosperm diversification. Am J Bot 96(1):336–348

    PubMed  Google Scholar 

  • Srivatsan SG (2004) Modeling prebiotic catalysis with nucleic acid-like polymers and its implications for the proposed RNA world. Pure Appl Chem 76(12):2085–2099

    CAS  Google Scholar 

  • Steitz JA, Dreyfuss G, Krainer AR, Lamond AI, Matera AG, Padgett RA (2008) Where in the cell is the minor spliceosome? Proc Natl Acad Sci U S A 105:8485–8486

    CAS  PubMed Central  PubMed  Google Scholar 

  • Stone JR, Wray GA (2001) Rapid evolution of cis-regulatory sequences via local point mutations. Mol Biol Evol 18:1764–1770

    CAS  PubMed  Google Scholar 

  • Strieker M, Tanovic A, Marahiel MA (2010) Nonribosomal peptide synthetases: structures and dynamics. Curr Opin Chem Biol 20:234–240

    CAS  Google Scholar 

  • Tate JA, Soltis DE, Soltis PS (2005) Polyploidy in plants. In: Gregory TR (ed) The evolution of the genome (Ch. 7). Elsevier, San Diego, pp 371–426

    Google Scholar 

  • The Potato Genome Sequencing Consortium (2011) Genome sequence and analysis of the tuber crop potato. Nature 475:189–197

    Google Scholar 

  • The Tomato Genome Consortium (2012) The tomato genome sequence provides insights into fleshy fruit evolution. Nature 485:635–641

    Google Scholar 

  • Tian Z, Rizzon C, Du J, Zhu L, Bennetzen JL, Jackson SA, Gaut BS, Ma J (2009) Do genetic recombination and gene density shape the pattern of DNA elimination in rice long terminal repeat retrotransposons? Genome Res 19:2221–2230

    CAS  PubMed Central  PubMed  Google Scholar 

  • Tinoco I, Chen G, Qu X (2010) RNA reactions one molecule at a time. Cold Spring Harb Perspect Biol. doi:10.1101/cshperspect.a003624

    PubMed Central  PubMed  Google Scholar 

  • Tornaletti S (2009) Transcription-coupled DNA repair: directing your effort where it’s most needed. Cell Mol Life Sci 66:1010–1020

    CAS  PubMed  Google Scholar 

  • Touchon M, Arneodo A, d’Aubenton-Carafa Y, Thermes C (2004) Transcription-coupled and splicing-coupled strand asymmetries in eukaryotic genomes. Nucleic Acids Res 32(17):4969–4978

    CAS  PubMed Central  PubMed  Google Scholar 

  • Trifonov EN (2004) The triplet code from first principles. J Biomol Struct Dyn 22(1):1–11

    CAS  PubMed  Google Scholar 

  • Tuch BB, Li H, Johnson AD (2008) Evolution of eukaryotic transcription circuits. Science 319:1797. doi:10.1126/science.1152398

    CAS  PubMed  Google Scholar 

  • Tümpel S, Maconochie M, Wiedemann LM, Krumlauf R (2002) Conservation and diversity in the cis-regulatory networks that integrate information controlling expression of Hoxa2 in hindbrain and cranial neural crest cells in vertebrates. Dev Biol 246:45–56

    PubMed  Google Scholar 

  • Uddin MN, Kim J-Y (2011) Non-cell-autonomous RNA silencing spread in plants. Bot Stud 52:129–136

    CAS  Google Scholar 

  • Ueno Y, Yurimoto H, Yoshioka H, Komiya T, Maruyama S (2002) Ion microprobe analysis of graphite from ca. 3.8 Ga metasediments, Isua crustal belt, West Greenland: relationship between metamorphism and carbon isotopic composition. Geochim Cosmochim Acta 66:1257–1268

    CAS  Google Scholar 

  • Van de Peer Y, Meyer A (2005) Large-scale gene and ancient genome duplications. In: Gregory TR (ed) The evolution of the genome (Ch. 6). Elsevier, San Diego, pp 329–368

    Google Scholar 

  • Vanyushin BF, Ashapkin VV (2011) DNA methylation in higher plants: past, present and future. Biochim Biophys Acta 1809:360–368

    CAS  PubMed  Google Scholar 

  • Varriale A, Bernardi G (2010) Distribution of DNA methylation, CpGs, and CpG islands in human isochores. Genomics 95:25–28

    CAS  PubMed  Google Scholar 

  • Voinnet O (2009) Origin, biogenesis, and activity of plant microRNAs. Cell 136:669–687

    CAS  PubMed  Google Scholar 

  • Voytek SB, Joyce GF (2007) Emergence of a fast-reacting ribozyme that is capable of undergoing continuous evolution. Proc Natl Acad Sci U S A 104:15288–15293

    CAS  PubMed Central  PubMed  Google Scholar 

  • Wächtershäuser G (1988) Before enzymes and templates: theory of surface metabolism. Microb Rev 52:452–484

    Google Scholar 

  • Wagner A (2009) Evolutionary constraints permeate large metabolic networks. BMC Evol Biol 9:231

    PubMed Central  PubMed  Google Scholar 

  • Walsh DA, Doolittle WF (2005) The real ‘domains’ of life. Curr Biol 15:R237–R240

    CAS  PubMed  Google Scholar 

  • Wang W, Brunet FG, Nevo E, Long M (2002) Origin of sphinx, a young chimeric RNA gene in Drosophila melanogaster. Proc Natl Acad Sci U S A 99:4448–4453

    CAS  PubMed Central  PubMed  Google Scholar 

  • Wang M, Yafremava LS, Caetano-Anollés D, Mittenthal JE, Caetano-Anollés G (2007) Reductive evolution of architectural repertoires in proteomes and the birth of the tripartite world. Genome Res 17:1572–1585

    PubMed Central  PubMed  Google Scholar 

  • Wochner A, Attwater J, Coulson A, Holliger P (2011) Ribozyme-catalyzed transcription of an active ribozyme. Science 332:209–212

    CAS  PubMed  Google Scholar 

  • Woese CR (1998) The universal ancestor. Proc Natl Acad Sci U S A 95:6854–6859

    CAS  PubMed Central  PubMed  Google Scholar 

  • Wolf YI, Koonin EV (2013) Genome reduction as the dominant mode of evolution. Bioessays 35:829–837

    PubMed Central  PubMed  Google Scholar 

  • Wray GA, Hahn MW, Abouheif E, Balhoff JP, Pizer M, Rockman MV, Romano LA (2003) The evolution of transcriptional regulation in eukaryotes. Mol Biol Evol 20(9):1377–1419

    CAS  PubMed  Google Scholar 

  • Wright MC, Joyce GF (1997) Continuous in vitro evolution of catalytic function. Science 276:614–617

    CAS  PubMed  Google Scholar 

  • Wu H, Zhang Z, Hu S, Yu J (2012) On the molecular mechanism of GC content variation among eubacterial genomes. Biol Direct 7:2

    CAS  PubMed Central  PubMed  Google Scholar 

  • WuG PMY, Conway SR, Wang JW, Weigel D, Poethig RS (2009) The sequential action of miR156 and miR172 regulates developmental timing in Arabidopsis. Cell 138:750–759

    Google Scholar 

  • Xia B, Bhatia S, Bubenheim B, Dadgar M, Densmore D, Anderson JC (2011) Developer’s and user’s guide to Clotho v2.0 A software platform for the creation of synthetic biological systems. Methods Enzymol 498:97–135

    CAS  PubMed  Google Scholar 

  • Yaish MWF, Peng M, Rothstein SJ (2009) AtMBD9 modulates Arabidopsis development through the dual epigenetic pathways of DNA methylation and histone acetylation. Plant J 59:123–135

    CAS  PubMed  Google Scholar 

  • Yang GD, Yan K, Wu BJ, Wang YH, Gao YX, Zheng CC (2012) Genome wide analysis of intronic microRNAs in rice and Arabidopsis. J Genet 91:313–324

    CAS  PubMed  Google Scholar 

  • Yarus M (2011) Getting past the RNA world: the initial Darwinian ancestor. Cold Spring Harb Perspect Biol 3:a003590

    PubMed Central  PubMed  Google Scholar 

  • Zaher HS, Unrau PJ (2007) Selection of an improved RNA polymerase ribozyme with superior extension and fidelity. RNA 13:1017–1026

    CAS  PubMed Central  PubMed  Google Scholar 

  • Zhang M, Kimatu JN, Xu K, Liu B (2010) DNA cytosine methylation in plant development. J Genet Genomics 37:1–12

    PubMed  Google Scholar 

  • Zhao X, Zhang Z, Yan J, Yu J (2007) GC content variability of eubacteria is governed by the pol III alpha subunit. Biochem Biophys Res Commun 356:20–25

    CAS  PubMed  Google Scholar 

  • Zoubak S, Clay O, Bernardi G (1996) The gene distribution of the human genome. Gene 174:95–102

    CAS  PubMed  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Nicolas Carels .

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2015 Springer India

About this chapter

Cite this chapter

Carels, N. (2015). A History of Genomic Structures: The Big Picture. In: Bahadur, B., Venkat Rajam, M., Sahijram, L., Krishnamurthy, K. (eds) Plant Biology and Biotechnology. Springer, New Delhi. https://doi.org/10.1007/978-81-322-2283-5_7

Download citation

Publish with us

Policies and ethics