Lander ES, Linton LM, Birren B, Nusbaum C, Zody MC, Baldwin J, Devon K, Dewar K, Doyle M, FitzHugh W, Funke R, Gage D, Harris K, Heaford A, Howland J, Kann L, Lehoczky J, LeVine R, McEwan P, McKernan K, Meldrim J, Mesirov JP, Miranda C, Morris W, Naylor J, Raymond C, Rosetti M, Santos R, Sheridan A, Sougnez C, et al: Initial sequencing and analysis of the human genome. Nature. 2001, 409: 860-921. 10.1038/35057062.
Article
CAS
PubMed
Google Scholar
Venter JC, Adams MD, Myers EW, Li PW, Mural RJ, Sutton GG, Smith HO, Yandell M, Evans CA, Holt RA, Gocayne JD, Amanatides P, Ballew RM, Huson DH, Wortman JR, Zhang Q, Kodira CD, Zheng XH, Chen L, Skupski M, Subramanian G, Thomas PD, Zhang J, Gabor Miklos GL, Nelson C, Broder S, Clark AG, Nadeau J, McKusick VA, Zinder N, et al: The sequence of the human genome. Science. 2001, 291: 1304-1351. 10.1126/science.1058040.
Article
CAS
PubMed
Google Scholar
Huda A, Jordan IK: Epigenetic regulation of mammalian genomes by transposable elements. Ann N Y Acad Sci. 2009, 1178: 276-284. 10.1111/j.1749-6632.2009.05007.x.
Article
CAS
PubMed
Google Scholar
López-Flores I, Garrido-Ramos MA: The repetitive DNA content of eukaryotic genomes. Genome Dyn. 2012, 7: 1-28.
Article
PubMed
Google Scholar
Defraia C, Slotkin RK: Analysis of retrotransposon activity in plants. Methods Mol Biol. 2014, 1112: 195-210. 10.1007/978-1-62703-773-0_13.
Article
CAS
PubMed
Google Scholar
Zedek F, Smerda J, Smarda P, Bures P: Correlated evolution of LTR retrotransposons and genome size in the genus Eleocharis. BMC Plant Biol. 2010, 10: 265-10.1186/1471-2229-10-265.
Article
CAS
PubMed Central
PubMed
Google Scholar
Carle P, Saillard C, Carrere N, Carrere S, Duret S, Eveillard S, Gaurivaud P, Gourgues G, Gouzy J, Salar P, Verdin E, Breton M, Blanchard A, Laigret F, Bové JM, Renaudin J, Foissac X: Partial chromosome sequence of Spiroplasma citri reveals extensive viral invasion and important gene decay. Appl Environ Microbiol. 2010, 76: 3420-3426. 10.1128/AEM.02954-09.
Article
CAS
PubMed Central
PubMed
Google Scholar
Casjens S: Prophages and bacterial genomics: what have we learned so far?. Mol Microbiol. 2003, 49: 277-300. 10.1046/j.1365-2958.2003.03580.x.
Article
CAS
PubMed
Google Scholar
Cambray G, Guerout AM, Mazel D: Integrons. Annu Rev Genet. 2010, 44: 141-166. 10.1146/annurev-genet-102209-163504.
Article
CAS
PubMed
Google Scholar
Hua-Van A, Le Rouzic A, Boutin TS, Filee J, Capy P: The struggle for life of the genome’s selfish architects. Biol Direct. 2011, 6: 19-10.1186/1745-6150-6-19.
Article
PubMed Central
PubMed
Google Scholar
Roberts AP, Mullany P: A modular master on the move: the Tn916 family of mobile genetic elements. Trends Microbiol. 2009, 17: 251-258. 10.1016/j.tim.2009.03.002.
Article
CAS
PubMed
Google Scholar
Grindley ND, Whiteson KL, Rice PA: Mechanisms of site-specific recombination. Annu Rev Biochem. 2006, 75: 567-605. 10.1146/annurev.biochem.73.011303.073908.
Article
CAS
PubMed
Google Scholar
Wicker T, Sabot F, Hua-Van A, Bennetzen JL, Capy P, Chalhoub B, Flavell A, Leroy P, Morgante M, Panaud O, Paux E, SanMiguel P, Schulman AH: A unified classification system for eukaryotic transposable elements. Nat Rev Genet. 2007, 8: 973-982. 10.1038/nrg2165.
Article
CAS
PubMed
Google Scholar
Kapitonov VV, Jurka J: A universal classification of eukaryotic transposable elements implemented in Repbase. Nat Rev Genet. 2008, 9: 411-412. 10.1038/nrg2165-c1. author reply 414
Article
PubMed
Google Scholar
Jurka J, Kapitonov VV, Kohany O, Jurka MV: Repetitive sequences in complex genomes: structure and evolution. Annu Rev Genomics Hum Genet. 2007, 8: 241-259. 10.1146/annurev.genom.8.080706.092416.
Article
CAS
PubMed
Google Scholar
Rice PA, Baker TA: Comparative architecture of transposase and integrase complexes. Nat Struct Biol. 2001, 8: 302-307. 10.1038/86166.
Article
CAS
Google Scholar
Chandler M, de la Cruz F, Dyda F, Hickman AB, Moncalian G, Ton-Hoang B: Breaking and joining single-stranded DNA: the HUH endonuclease superfamily. Nat Rev Microbiol. 2013, 11: 525-538. 10.1038/nrmicro3067.
Article
CAS
PubMed
Google Scholar
Ilyina TV, Koonin EV: Conserved sequence motifs in the initiator proteins for rolling circle DNA replication encoded by diverse replicons from eubacteria, eucaryotes and archaebacteria. Nucleic Acids Res. 1992, 20: 3279-3285. 10.1093/nar/20.13.3279.
Article
CAS
PubMed Central
PubMed
Google Scholar
Krupovic M: Networks of evolutionary interactions underlying the polyphyletic origin of ssDNA viruses. Curr Opin Virol. 2013, 3: 578-586. 10.1016/j.coviro.2013.06.010.
Article
CAS
PubMed
Google Scholar
Goodwin TJ, Butler MI, Poulter RT: Cryptons: a group of tyrosine-recombinase-encoding DNA transposons from pathogenic fungi. Microbiology. 2003, 149: 3099-3109. 10.1099/mic.0.26529-0.
Article
CAS
PubMed
Google Scholar
Goodwin TJ, Poulter RT: A new group of tyrosine recombinase-encoding retrotransposons. Mol Biol Evol. 2004, 21: 746-759. 10.1093/molbev/msh072.
Article
CAS
PubMed
Google Scholar
Boocock MR, Rice PA: A proposed mechanism for IS607-family serine transposases. Mob DNA. 2013, 4: 24-10.1186/1759-8753-4-24.
Article
PubMed Central
PubMed
Google Scholar
Koonin EV, Dolja VV: A virocentric perspective on the evolution of life. Curr Opin Virol. 2013, 3: 546-557. 10.1016/j.coviro.2013.06.008.
Article
PubMed Central
PubMed
Google Scholar
Krupovic M, Bamford DH, Koonin EV: Conservation of major and minor jelly-roll capsid proteins in Polinton (Maverick) transposons suggests that they are bona fide viruses. Biol Direct. 2014, 9: 6-10.1186/1745-6150-9-6.
Article
PubMed Central
PubMed
Google Scholar
Malik HS, Henikoff S, Eickbush TH: Poised for contagion: evolutionary origins of the infectious abilities of invertebrate retroviruses. Genome Res. 2000, 10: 1307-1318. 10.1101/gr.145000.
Article
CAS
PubMed
Google Scholar
Kapitonov VV, Jurka J: Self-synthesizing DNA transposons in eukaryotes. Proc Natl Acad Sci U S A. 2006, 103: 4540-4545. 10.1073/pnas.0600833103.
Article
CAS
PubMed Central
PubMed
Google Scholar
Pritham EJ, Putliwala T, Feschotte C: Mavericks, a novel class of giant transposable elements widespread in eukaryotes and related to DNA viruses. Gene. 2007, 390: 3-17. 10.1016/j.gene.2006.08.008.
Article
CAS
PubMed
Google Scholar
Labrie SJ, Samson JE, Moineau S: Bacteriophage resistance mechanisms. Nat Rev Microbiol. 2010, 8: 317-327. 10.1038/nrmicro2315.
Article
CAS
PubMed
Google Scholar
Makarova KS, Wolf YI, Koonin EV: Comparative genomics of defense systems in archaea and bacteria. Nucleic Acids Res. 2013, 41: 4360-4377. 10.1093/nar/gkt157.
Article
CAS
PubMed Central
PubMed
Google Scholar
Westra ER, Swarts DC, Staals RH, Jore MM, Brouns SJ, van der Oost J: The CRISPRs, they are a-changin’: how prokaryotes generate adaptive immunity. Annu Rev Genet. 2012, 46: 311-339. 10.1146/annurev-genet-110711-155447.
Article
CAS
PubMed
Google Scholar
Barrangou R: CRISPR-Cas systems and RNA-guided interference. Wiley Interdiscip Rev RNA. 2013, 4: 267-278. 10.1002/wrna.1159.
Article
CAS
PubMed
Google Scholar
Makarova KS, Aravind L, Wolf YI, Koonin EV: Unification of Cas protein families and a simple scenario for the origin and evolution of CRISPR-Cas systems. Biol Direct. 2011, 6: 38-10.1186/1745-6150-6-38.
Article
CAS
PubMed Central
PubMed
Google Scholar
Makarova KS, Wolf YI, Koonin EV: The basic building blocks and evolution of CRISPR-cas systems. Biochem Soc Trans. 2013, 41: 1392-1400.
Article
CAS
PubMed
Google Scholar
Datsenko KA, Pougach K, Tikhonov A, Wanner BL, Severinov K, Semenova E: Molecular memory of prior infections activates the CRISPR/Cas adaptive bacterial immunity system. Nat Commun. 2012, 3: 945-
Article
PubMed
Google Scholar
Makarova KS, Haft DH, Barrangou R, Brouns SJ, Charpentier E, Horvath P, Moineau S, Mojica FJ, Wolf YI, Yakunin AF, van der Oost J, Koonin EV: Evolution and classification of the CRISPR-Cas systems. Nat Rev Microbiol. 2011, 9: 467-477. 10.1038/nrmicro2577.
Article
CAS
PubMed
Google Scholar
Yosef I, Goren MG, Qimron U: Proteins and DNA elements essential for the CRISPR adaptation process in Escherichia coli. Nucleic Acids Res. 2012, 40: 5569-5576. 10.1093/nar/gks216.
Article
CAS
PubMed Central
PubMed
Google Scholar
Babu M, Beloglazova N, Flick R, Graham C, Skarina T, Nocek B, Gagarinova A, Pogoutse O, Brown G, Binkowski A, Phanse S, Joachimiak A, Koonin EV, Savchenko A, Emili A, Greenblatt J, Edwards AM, Yakunin AF: A dual function of the CRISPR-Cas system in bacterial antivirus immunity and DNA repair. Mol Microbiol. 2011, 79: 484-502. 10.1111/j.1365-2958.2010.07465.x.
Article
CAS
PubMed Central
PubMed
Google Scholar
Díez-Villaseñor C, Guzmán NM, Almendros C, García-Martínez J, Mojica FJ: CRISPR-spacer integration reporter plasmids reveal distinct genuine acquisition specificities among CRISPR-Cas I-E variants of Escherichia coli. RNA Biol. 2013, 10: 792-802. 10.4161/rna.24023.
Article
PubMed Central
PubMed
Google Scholar
Kim TY, Shin M, Huynh Thi Yen L, Kim JS: Crystal structure of Cas1 from Archaeoglobus fulgidus and characterization of its nucleolytic activity. Biochem Biophys Res Commun. 2013, 441: 720-725. 10.1016/j.bbrc.2013.10.122.
Article
CAS
PubMed
Google Scholar
Wiedenheft B, Zhou K, Jinek M, Coyle SM, Ma W, Doudna JA: Structural basis for DNase activity of a conserved protein implicated in CRISPR-mediated genome defense. Structure. 2009, 17: 904-912. 10.1016/j.str.2009.03.019.
Article
CAS
PubMed
Google Scholar
Mahillon J, Chandler M: Insertion sequences. Microbiol Mol Biol Rev. 1998, 62: 725-774.
CAS
PubMed Central
PubMed
Google Scholar
Kojima KK, Jurka J: A superfamily of DNA transposons targeting multicopy small RNA genes. PLoS One. 2013, 8: e68260-10.1371/journal.pone.0068260.
Article
CAS
PubMed Central
PubMed
Google Scholar
Peters JE, Craig NL: Tn7: smarter than we thought. Nat Rev Mol Cell Biol. 2001, 2: 806-814. 10.1038/35099006.
Article
CAS
PubMed
Google Scholar
Parks AR, Peters JE: Tn7 elements: engendering diversity from chromosomes to episomes. Plasmid. 2009, 61: 1-14. 10.1016/j.plasmid.2008.09.008.
Article
CAS
PubMed Central
PubMed
Google Scholar
Könneke M, Bernhard AE, de la Torre JR, Walker CB, Waterbury JB, Stahl DA: Isolation of an autotrophic ammonia-oxidizing marine archaeon. Nature. 2005, 437: 543-546. 10.1038/nature03911.
Article
PubMed
Google Scholar
Park SJ, Kim JG, Jung MY, Kim SJ, Cha IT, Ghai R, Martin-Cuadrado AB, Rodriguez-Valera F, Rhee SK: Draft genome sequence of an ammonia-oxidizing archaeon, “Candidatus Nitrosopumilus sediminis” AR2, from Svalbard in the Arctic Circle. J Bacteriol. 2012, 194: 6948-6949. 10.1128/JB.01869-12.
Article
CAS
PubMed Central
PubMed
Google Scholar
Bath C, Cukalac T, Porter K, Dyall-Smith ML: His1 and His2 are distantly related, spindle-shaped haloviruses belonging to the novel virus group, Salterprovirus. Virology. 2006, 350: 228-239. 10.1016/j.virol.2006.02.005.
Article
CAS
PubMed
Google Scholar
Krupovic M, Quemin ER, Bamford DH, Forterre P, Prangishvili D: Unification of the globally distributed spindle-shaped viruses of the Archaea. J Virol. 2014, 88: 2354-2358. 10.1128/JVI.02941-13.
Article
PubMed Central
PubMed
Google Scholar
Pietilä MK, Atanasova NS, Manole V, Liljeroos L, Butcher SJ, Oksanen HM, Bamford DH: Virion architecture unifies globally distributed pleolipoviruses infecting halophilic archaea. J Virol. 2012, 86: 5067-5079. 10.1128/JVI.06915-11.
Article
PubMed Central
PubMed
Google Scholar
Gorlas A, Robert C, Gimenez G, Drancourt M, Raoult D: Complete genome sequence of Methanomassiliicoccus luminyensis, the largest genome of a human-associated Archaea species. J Bacteriol. 2012, 194: 4745-10.1128/JB.00956-12.
Article
CAS
PubMed Central
PubMed
Google Scholar
Reysenbach AL, Liu Y, Banta AB, Beveridge TJ, Kirshtein JD, Schouten S, Tivey MK, Von Damm KL, Voytek MA: A ubiquitous thermoacidophilic archaeon from deep-sea hydrothermal vents. Nature. 2006, 442: 444-447. 10.1038/nature04921.
Article
CAS
PubMed
Google Scholar
Filée J, Forterre P, Sen-Lin T, Laurent J: Evolution of DNA polymerase families: evidences for multiple gene exchange between cellular and viral proteins. J Mol Evol. 2002, 54: 763-773. 10.1007/s00239-001-0078-x.
Article
PubMed
Google Scholar
Tahirov TH, Makarova KS, Rogozin IB, Pavlov YI, Koonin EV: Evolution of DNA polymerases: an inactivated polymerase-exonuclease module in Pol epsilon and a chimeric origin of eukaryotic polymerases from two classes of archaeal ancestors. Biol Direct. 2009, 4: 11-10.1186/1745-6150-4-11.
Article
PubMed Central
PubMed
Google Scholar
Andrade MA, Petosa C, O’Donoghue SI, Muller CW, Bork P: Comparison of ARM and HEAT protein repeats. J Mol Biol. 2001, 309: 1-18. 10.1006/jmbi.2001.4624.
Article
CAS
PubMed
Google Scholar
Iyer LM, Leipe DD, Koonin EV, Aravind L: Evolutionary history and higher order classification of AAA + ATPases. J Struct Biol. 2004, 146: 11-31. 10.1016/j.jsb.2003.10.010.
Article
CAS
PubMed
Google Scholar
Bell SD, Botting CH, Wardleworth BN, Jackson SP, White MF: The interaction of Alba, a conserved archaeal chromatin protein, with Sir2 and its regulation by acetylation. Science. 2002, 296: 148-151. 10.1126/science.1070506.
Article
CAS
PubMed
Google Scholar
Aravind L, Iyer LM, Leipe DD, Koonin EV: A novel family of P-loop NTPases with an unusual phyletic distribution and transmembrane segments inserted within the NTPase domain. Genome Biol. 2004, 5: R30-10.1186/gb-2004-5-5-r30.
Article
CAS
PubMed Central
PubMed
Google Scholar
Filée J, Siguier P, Chandler M: Insertion sequence diversity in archaea. Microbiol Mol Biol Rev. 2007, 71: 121-157. 10.1128/MMBR.00031-06.
Article
PubMed Central
PubMed
Google Scholar
Klassen R, Meinhardt F: Linear protein-primed replicating plasmids in eukaryotic microbes. Microbiol Monogr. 2007, 7: 188-216.
Google Scholar
Salas M: Protein-priming of DNA replication. Annu Rev Biochem. 1991, 60: 39-71. 10.1146/annurev.bi.60.070191.000351.
Article
CAS
PubMed
Google Scholar
Krupovic M, Koonin EV: Evolution of eukaryotic single-stranded DNA viruses of the Bidnaviridae family from genes of four other groups of widely different viruses. Sci Rep. 2014, in press
Google Scholar
Nunez JK, Kranzusch PJ, Noeske J, Wright AV, Davies CW, Doudna JA: Cas1-Cas2 complex formation mediates spacer acquisition during CRISPR-Cas adaptive immunity. Nat Struct Mol Biol. 2014, doi:10.1038/nsmb.2820
Google Scholar
Chylinski K, Makarova KS, Charpentier E, Koonin EV: Classification and evolution of the protein and RNA components of type II CRISPR-Cas systems. Nucleic Acids Res. in press
Kapitonov VV, Jurka J: RAG1 core and V(D)J recombination signal sequences were derived from Transib transposons. PLoS Biol. 2005, 3: e181-10.1371/journal.pbio.0030181.
Article
PubMed Central
PubMed
Google Scholar
Forterre P, Prangishvili D: The major role of viruses in cellular evolution: facts and hypotheses. Curr Opin Virol. 2013, 3: 558-565. 10.1016/j.coviro.2013.06.013.
Article
CAS
PubMed
Google Scholar
Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ: Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 1997, 25: 3389-3402. 10.1093/nar/25.17.3389.
Article
CAS
PubMed Central
PubMed
Google Scholar
Marchler-Bauer A, Bryant SH: CD-Search: protein domain annotations on the fly. Nucleic Acids Res. 2004, 32: W327-W331. 10.1093/nar/gkh454.
Article
CAS
PubMed Central
PubMed
Google Scholar
Söding J: Protein homology detection by HMM-HMM comparison. Bioinformatics. 2005, 21: 951-960. 10.1093/bioinformatics/bti125.
Article
PubMed
Google Scholar
Okonechnikov K, Golosova O, Fursov M: Unipro UGENE: a unified bioinformatics toolkit. Bioinformatics. 2012, 28: 1166-1167. 10.1093/bioinformatics/bts091.
Article
CAS
PubMed
Google Scholar
Zuker M: Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res. 2003, 31: 3406-3415. 10.1093/nar/gkg595.
Article
CAS
PubMed Central
PubMed
Google Scholar
Siguier P, Perochon J, Lestrade L, Mahillon J, Chandler M: ISfinder: the reference centre for bacterial insertion sequences. Nucleic Acids Res. 2006, 34: D32-D36. 10.1093/nar/gkj014.
Article
CAS
PubMed Central
PubMed
Google Scholar
Pei J, Kim BH, Grishin NV: PROMALS3D: a tool for multiple protein sequence and structure alignments. Nucleic Acids Res. 2008, 36: 2295-2300. 10.1093/nar/gkn072.
Article
CAS
PubMed Central
PubMed
Google Scholar
Edgar RC: MUSCLE: a multiple sequence alignment method with reduced time and space complexity. BMC Bioinformatics. 2004, 5: 113-10.1186/1471-2105-5-113.
Article
PubMed Central
PubMed
Google Scholar
Jurka J, Kapitonov VV, Pavlicek A, Klonowski P, Kohany O, Walichiewicz J: Repbase Update, a database of eukaryotic repetitive elements. Cytogenet Genome Res. 2005, 110: 462-467. 10.1159/000084979.
Article
CAS
PubMed
Google Scholar
Yutin N, Makarova KS, Mekhedov SL, Wolf YI, Koonin EV: The deep archaeal roots of eukaryotes. Mol Biol Evol. 2008, 25: 1619-1630. 10.1093/molbev/msn108.
Article
CAS
PubMed Central
PubMed
Google Scholar
Price MN, Dehal PS, Arkin AP: FastTree: computing large minimum evolution trees with profiles instead of a distance matrix. Mol Biol Evol. 2009, 26: 1641-1650. 10.1093/molbev/msp077.
Article
CAS
PubMed Central
PubMed
Google Scholar
Tamura K, Stecher G, Peterson D, Filipski A, Kumar S: MEGA6: Molecular Evolutionary Genetics Analysis version 6.0. Mol Biol Evol. 2013, 30: 2725-2729. 10.1093/molbev/mst197.
Article
CAS
PubMed Central
PubMed
Google Scholar