CoChat
Sign Up
Cited by 283Chromosomal and Genetic VariationsGenomics and Phylogenetic StudiesGenome Rearrangement Algorithms

Evolution and Diversity of Transposable Elements in Vertebrate Genomes

Open access
Sotero-Caio, Cibele G., Platt, Roy N., Suh, Alexander, Ray, David A.·2017·Genome Biology and Evolution
DOI 10.1093/gbe/evw264PMC PMC5381603
Open this paper in CoChat — free accountOpen PDF

Abstract

Transposable elements (TEs) are selfish genetic elements that mobilize in genomes via transposition or retrotransposition and often make up large fractions of vertebrate genomes. Here, we review the current understanding of vertebrate TE diversity and evolution in the context of recent advances in genome sequencing and assembly techniques. TEs make up 4-60% of assembled vertebrate genomes, and deeply branching lineages such as ray-finned fishes and amphibians generally exhibit a higher TE diversity than the more recent radiations of birds and mammals. Furthermore, the list of taxa with exceptional TE landscapes is growing. We emphasize that the current bottleneck in genome analyses lies in the proper annotation of TEs and provide examples where superficial analyses led to misleading conclusions about genome evolution. Finally, recent advances in long-read sequencing will soon permit access to TE-rich genomic regions that previously resisted assembly including the gigantic, TE-rich genomes of salamanders and lungfishes.

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Integrity signals

Registry

Crossref · 10.1093/gbe/evw264

Cites

7 of 7 references verified0 citation errors · 0 not checkable

Statistics

Claims the paper makes

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Claims other papers make about this one

Each is checked against this paper’s own text: does it say what the citing paper says it does?

  • The primary causes of TE depletion were reduction of LTR elements and DNA transposons, which are highly active element classes capable of rapid genome expansion.

    “The primary causes of TE depletion were reduction of LTR elements and DNA transposons which are highly active element classes capable of rapid genome expansion (57–62).”

    From Convergent genome streamlining accompanies independent miniaturization in the world’s smallest fishes (2026) · cites this paper as [61]

    The Introduction says TE content is linked to genome size, and The Future links LTR retrotransposons to large salamander genomes; the Eutheria section describes substantial DNA-transposon accumulation in bats. These passages support the capacity of these elements to expand genomes, but the paper does not identify reductions in LTR elements and DNA transposons as the primary causes of the claimed TE depletion. (LLM, conf=0.84)

    Experimental — accuracy not yet measured

  • Low-divergence copies of transposable elements represent more recent insertions, and highly diverged copies reflect older, inactive elements.

    “Low-divergence copies represent more recent insertions and highly diverged copies reflect older, inactive elements (53, 57, 61).”

    From Convergent genome streamlining accompanies independent miniaturization in the world’s smallest fishes (2026) · cites this paper as [61]

    The Squamata section (page unavailable) links genetic distance with recent TE activity and describes older elements as more heavily mutated. The Annotating TEs section also says overestimated divergence makes TE accumulations appear older. Neither passage establishes that highly diverged copies are necessarily inactive, so that part of the claim is unsupported. (LLM, conf=0.83)

    Experimental — accuracy not yet measured

Self-check

Percentages, sums and reported differences re-computed from the paper’s own numbers.

The self-check needs the paper’s full text.

Cites

Flagged first, then by citations

Research works printed but not linked: 220

  1. Acosta MJ Marchal JA Fernández-Espartero CH Bullejos M Sánchez A. 2008 Retroelements (LINEs and SINEs) in vole genomes: differential distribution in the constitutive heterochromatin. Chromosome Res. 16: 949– 959. 18836842
  2. Adelson DL Raison JM Edgar RC. 2009 Characterization and distribution of retrotransposons and simple sequence repeats in the bovine genome. Proc Natl Acad Sci U S A. 106: 12855– 12860. 19625614 PMC2722308
  3. Akagi K Li J Stephens RM Volfovsky N Symer DE. 2008 Extensive variation between inbred mouse strains due to endogenous L1 retrotransposition. Genome Res. 18: 869– 880. 18381897 PMC2413154
  4. Alföldi J, 2011 The genome of the green anole lizard and a comparative analysis with birds and mammals. Nature 477: 587– 591. 21881562 PMC3184186
  5. Amemiya CT, 2013 The African coelacanth genome provides insights into tetrapod evolution. Nature 496: 311– 316. 23598338 PMC3633110
  6. Aparicio S, 2002 Whole-genome shotgun assembly and analysis of the genome of Fugu rubripes. Science 297: 1301– 1310. 12142439
  7. Bao W Jurka MG Kapitonov VV Jurka J. 2009 New superfamilies of eukaryotic DNA transposons and their internal divisions. Mol Biol Evol. 26: 983– 993. 19174482 PMC2727372
  8. Bejerano G, 2006 A distal enhancer and an ultraconserved exon are derived from a novel retroposon. Nature 441: 87– 90. 16625209
  9. Bénit L Lallemand J-B Casella J-F Philippe H Heidmann T. 1999 ERV-L elements: a family of endogenous retrovirus-like elements active throughout the evolution of mammals. J Virol. 73: 3301– 3308. 10074184 PMC104094
  10. Bergman CM Bensasson D. 2007 Recent LTR retrotransposon insertion contrasts with waves of non-LTR insertion since speciation in Drosophila melanogaster. Proc Natl Acad Sci U S A. 104: 11340– 11345. 17592135 PMC2040900
  11. Berthelot C, 2014 The rainbow trout genome provides novel insights into evolution after whole-genome duplication in vertebrates. Nat Commun. 5: 3657. 24755649 PMC4071752
  12. Biscotti MA, 2016 The Lungfish Transcriptome: a glimpse into molecular evolution events at the transition from water to land. Sci Rep. 6: 21571. 26908371 PMC4764851
  13. Blass E Bell M Boissinot S. 2012 Accumulation and rapid decay of non-LTR retrotransposons in the genome of the three-spine stickleback. Genome Biol Evol. 4: 687– 702. 22534163 PMC3381678
  14. Boer JGD Yazawa R Davidson WS Koop BF. 2007 Bursts and horizontal evolution of DNA transposons in the speciation of pseudotetraploid salmonids. BMC Genomics 8: 422. 18021408 PMC2198921
  15. Böhne A, 2012 Zisupton—a novel superfamily of DNA transposable elements recently active in fish. Mol Biol Evol. 29: 631– 645. 21873630
  16. Boissinot S Furano AV. 2001 Adaptive evolution in LINE-1 retrotransposons. Mol Biol Evol. 18: 2186– 2194. 11719568
  17. Braasch I, 2016 The spotted gar genome illuminates vertebrate evolution and facilitates human-teleost comparisons. Nat Genet. 48: 427– 437. 26950095 PMC4817229
  18. Brawand D, 2014 The genomic substrate for adaptive radiation in African cichlid fish. Nature 513: 375– 381. 25186727 PMC4353498
  19. Cantrell MA, 2005 MysTR: an endogenous retrovirus family in mammals that is undergoing recent amplifications to unprecedented copy numbers. J Virol. 79: 14698– 14707. 16282470 PMC1287555
  20. Cantrell MA Scott L Brown CJ Martinez AR Wichman HA. 2008 Loss of LINE-1 activity in the megabats. Genetics 178: 393– 404. 18202382 PMC2206088
  21. Carbone L, 2014 Gibbon genome and the fast karyotype evolution of small apes. Nature 513: 195– 201. 25209798 PMC4249732
  22. Casavant NC, 2000 The end of the LINE?: lack of recent L1 activity in a group of South American rodents. Genetics 154: 1809– 1817. 10747071 PMC1461046
  23. Casola C Hucks D Feschotte C. 2008 Convergent domestication of pogo-like transposases into centromere-binding proteins in fission yeast and mammals. Mol Biol Evol. 25: 29– 41. 17940212 PMC2268608
  24. Castoe TA, 2013 The Burmese python genome reveals the molecular basis for extreme adaptation in snakes. Proc Natl Acad Sci U S A. 110: 20645– 20650. 24297902 PMC3870669
  25. Castoe TA, 2011 Discovery of highly divergent repeat landscapes in snake genomes using high-throughput sequencing. Genome Biol Evol. 3: 641– 653. PMC3157835 21572095
  26. Chalopin D, 2014 Evolutionary active transposable elements in the genome of the coelacanth. J Exp Zool B Mol Dev Evol. 322: 322– 333. 23908136
  27. Chalopin D Naville M Plard F Galiana D Volff J-N. 2015 Comparative analysis of transposable elements highlights mobilome diversity and evolution in vertebrates. Genome Biol Evol. 7: 567– 580. 25577199 PMC4350176
  28. Chénais B Caruso A Hiard S Casse N. 2012 The impact of transposable elements on eukaryotic genomes: from genome size increase to genetic adaptation to stressful environments. Gene 509: 7– 15. 22921893
  29. Chong AY, 2014 Evolution and gene capture in ancient endogenous retroviruses-insights from the crocodilian genomes. Retrovirology 11: 71. 25499090 PMC4299795
  30. Chuong EB Elde NC Feschotte C. 2016 Regulatory evolution of innate immunity through co-option of endogenous retroviruses. Science 351: 1083– 1087. 26941318 PMC4887275
  31. Churakov G, 2010 Rodent evolution: back to the root. Mol Biol Evol. 27: 1315– 1326. 20100942
  32. Church DM, 2009 Lineage-specific biology revealed by a finished genome assembly of the mouse. PLoS Biol. 7: e1000112. 19468303 PMC2680341
  33. Crollius HR, 2000 Characterization and repeat analysis of the compact genome of the freshwater pufferfish Tetraodon nigroviridis. Genome Res. 10: 939– 949. 10899143 PMC310905
  34. Cui J, 2014 Low frequency of paleoviral infiltration across the avian phylogeny. Genome Biol. 15: 539. 25496498 PMC4272516
  35. Daniels SB Peterson KR Strausbaugh LD Kidwell MG Chovnick A. 1990 Evidence for horizontal transmission of the P transposable element between Drosophila species. Genetics 124: 339– 355. 2155157 PMC1203926
  36. de Koning AJ Gu W Castoe TA Batzer MA Pollock DD. 2011 Repetitive elements may comprise over two-thirds of the human genome. PLoS Genet. 7: e1002384. 22144907 PMC3228813
  37. Deininger PL Batzer MA. 2002 Mammalian retroelements. Genome Res. 12: 1455– 1465. 12368238
  38. Duvernell DD Pryor SR Adams SM. 2004 Teleost fish genomes contain a diverse array of l1 retrotransposon lineages that exhibit a low copy number and high rate of turnover. J Mol Evol. 59: 298– 308. 15553085
  39. Eickbush T Malik H. 2002 Origins and evolution of retrotransposons In: Craig NL Craigie R Gellert M Lambowitz AM, editors. Mobile DNA II. Washington, DC: ASM Press p. 1111– 1144.
  40. Eickbush TH Jamburuthugoda VK. 2008 The diversity of retrotransposons and the properties of their reverse transcriptases. Virus Res. 134: 221– 234. 18261821 PMC2695964
  41. Eid J, 2009 Real-time DNA sequencing from single polymerase molecules. Science 323: 133– 138. 19023044
  42. Elliott TA Gregory TR. 2015 What's in a genome? The C-value enigma and the evolution of eukaryotic genome content. Philos Trans R Soc B. 370: 20140331. PMC4571570 26323762
  43. Endoh H Okada N. 1986 Total DNA transcription in vitro: a procedure to detect highly repetitive and transcribable sequences with tRNA-like structures. Proc Natl Acad Sci U S A. 83: 251– 255. 3455763 PMC322835
  44. Erickson IK Cantrell MA Scott L Wichman HA. 2011 Retrofitting the genome: L1 extinction follows endogenous retroviral expansion in a group of muroid rodents. J Virol. 85: 12315– 12323. 21957310 PMC3209412
  45. Farré M Robinson TJ Ruiz‐Herrera A. 2015 An Integrative Breakage Model of genome architecture, reshuffling and evolution. Bioessays 37: 479– 488. 25739389
  46. Feschotte C Pritham EJ. 2007 DNA transposons and the evolution of eukaryotic genomes. Annu Rev Genet. 41: 331. 18076328 PMC2167627
  47. Finnegan DJ. 1989 Eukaryotic transposable elements and genome evolution. Trends Genet. 5: 103– 107. 2543105
  48. Foote AD, 2015 Convergent evolution of the genomes of marine mammals. Nat Genet. 47: 272– 275. 25621460 PMC4644735
  49. Forconi M, 2014 Transcriptional activity of transposable elements in coelacanth. J Exp Zool B Mol Dev Evol. 322: 379– 389. 24038780
  50. Furano AV Duvernell DD Boissinot S. 2004 L1 (LINE-1) retrotransposon diversity differs dramatically between mammals and fish. Trends Genet. 20: 9– 14. 14698614
  51. Gao B, 2016 The contribution of transposable elements to size variations between four teleost genomes. Mobile DNA 7: 4. 26862351 PMC4746887
  52. Ge R-L, 2013 Draft genome sequence of the Tibetan antelope. Nat Commun. 4: 1858. 23673643 PMC3674232
  53. Gentles AJ, 2007 Evolutionary dynamics of transposable elements in the short-tailed opossum Monodelphis domestica. Genome Res. 17: 992– 1004. 17495012 PMC1899126
  54. Georges A, 2015 High-coverage sequencing and annotated assembly of the genome of the Australian dragon lizard Pogona vitticeps. GigaScience 4(1): 11. 26421146 PMC4585809
  55. Gilbert C Hernandez SS Flores-Benabib J Smith EN Feschotte C. 2011 Rampant horizontal transfer of SPIN transposons in squamate reptiles. Mol Biol Evol. 29: 503– 515. 21771716 PMC3350315
  56. Gilbert C Schaack S Pace JK II Brindley PJ Feschotte C. 2010 A role for host-parasite interactions in the horizontal transfer of transposons across phyla. Nature 464: 1347– 1350. 20428170 PMC3004126
  57. Gilbert C Waters P Feschotte C Schaack S. 2013 Horizontal transfer of OC1 transposons in the Tasmanian devil. BMC Genomics 14: 134. 23445260 PMC3621081
  58. Gogolevsky KP Vassetzky NS Kramerov DA. 2009 5S rRNA-derived and tRNA-derived SINEs in fruit bats. Genomics 93: 494– 500. 19442632
  59. Gordon D, 2016 Long-read sequence assembly of the gorilla genome. Science 352: aae0344. 27034376 PMC4920363
  60. Goubert C, 2015 De novo assembly and annotation of the Asian tiger mosquito (Aedes albopictus) repeatome with dnaPipeTE from raw genomic reads and comparative analysis with the yellow fever mosquito (Aedes aegypti). Genome Biol Evol. 7: 1192– 1205. 25767248 PMC4419797
  61. Grabundzija I, 2016 A Helitron transposon reconstructed from bats reveals a novel mechanism of genome shuffling in eukaryotes. Nat Commun. 7: 10716. 26931494 PMC4778049
  62. Grahn R Rinehart T Cantrell M Wichman H. 2005 Extinction of LINE-1 activity coincident with a major mammalian radiation in rodents. Cytogenet Genome Res. 110: 407– 415. 16093693
  63. Gray YH. 2000 It takes two transposons to tango: transposable-element-mediated chromosomal rearrangements. Trends Genet. 16: 461– 468. 11050333
  64. Green RE, 2014 Three crocodilian genomes reveal ancestral patterns of evolution among archosaurs. Science 346: 1254449. 25504731 PMC4386873
  65. Gregory TR. 2002 Genome size and developmental complexity. Genetica 115: 131– 146. 12188045
  66. Hartl D Lozovskaya E Lawrence J. 1992 Nonautonomous transposable elements in prokaryotes and eukaryotes. Genetica 86: 47– 53. 1334917
  67. Hedges D Deininger P. 2007 Inviting instability: transposable elements, double-strand breaks, and the maintenance of genome integrity. Mutat Res/Fundam Mol Mech Mutagenesis 616: 46– 59. PMC1850990 17157332
  68. Hedges DJ, 2004 Differential Alu mobilization and polymorphism among the human and chimpanzee lineages. Genome Res. 14: 1068– 1075. 15173113 PMC419785
  69. Hellsten U, 2010 The genome of the Western clawed frog Xenopus tropicalis. Science 328: 633– 636. 20431018 PMC2994648
  70. Herniou E, 1998 Retroviral diversity and distribution in vertebrates. J Virol. 72: 5955– 5966. 9621058 PMC110400
  71. Hillier LW, 2004 Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution. Nature 432: 695– 716. 15592404
  72. Hoen DR, 2015 A call for benchmarking transposable element annotation methods. Mobile DNA 6(1): PMC4524446 26244060
  73. Howe K, 2013 The zebrafish reference genome sequence and its relationship to the human genome. Nature 496: 498– 503. 23594743 PMC3703927
  74. Jurka J Bao W Kojima KK. 2011 Families of transposable elements, population structure and the origin of species. Biol Direct. 6(1): 16. 21929767 PMC3183009
  75. Jurka J Bao W Kojima KK Kohany O Yurka MG. 2012 Distinct groups of repetitive families preserved in mammals correspond to different periods of regulatory innovations in vertebrates. Biol Direct. 7: 36. 23098210 PMC3500645
  76. Kaiser VB van Tuinen M Ellegren H. 2007 Insertion events of CR1 retrotransposable elements elucidate the phylogenetic branching order in galliform birds. Mol Biol Evol. 24: 338– 347. 17077154
  77. Kajikawa M Ohshima K Okada N. 1997 Determination of the entire sequence of turtle CR1: the first open reading frame of the turtle CR1 element encodes a protein with a novel zinc finger motif. Mol Biol Evol. 14: 1206– 1217. 9402732
  78. Kajikawa M Okada N. 2002 LINEs mobilize SINEs in the eel through a shared 3′ sequence. Cell 111: 433– 444. 12419252
  79. Kambol R Abtholuddin MF. 2008 Genome structure and characterisation of an endogenous retrovirus from the zebrafish genome project database. New York: Springer.
  80. Kapitonov VV Jurka J. 2005 RAG1 core and V (D) J recombination signal sequences were derived from Transib transposons. PLoS Biol. 3: 998. PMC1131882 15898832
  81. Kapitonov VV Jurka J. 2001 Rolling-circle transposons in eukaryotes. Proc Natl Acad Sci U S A. 98: 8714– 8719. 11447285 PMC37501
  82. Kapitonov VV Jurka J. 2006 Self-synthesizing DNA transposons in eukaryotes. Proc Natl Acad Sci U S A. 103: 4540– 4545. 16537396 PMC1450207
  83. Kapitonov VV Jurka J. 2008 A universal classification of eukaryotic transposable elements implemented in Repbase. Nat Rev Genet. 9: 411– 412. 18421312
  84. Kapusta A Suh A 2016. Evolution of bird genomes–a transposon’s-eye view. Ann N Y Acad Sci. Advance Access published December 20, 2016, doi:10.1111/nyas.13295. 27997700 · DOI
  85. Kasahara M, 2007 The medaka draft genome and insights into vertebrate genome evolution. Nature 447: 714– 719. 17554307
  86. Kass DH Jamison N. 2007 Identification of an active ID-like group of SINEs in the mouse. Genomics 90: 416– 420. 17572061 PMC2034284
  87. Kass DH Raynor ME Williams TM. 2000 Evolutionary history of B1 retroposons in the genus Mus. J Mol Evol. 51: 256– 264. 11029070
  88. Keinath MC, 2015 Initial characterization of the large genome of the salamander Ambystoma mexicanum using shotgun and laser capture chromosome sequencing. Sci Rep. 5: 1–13. PMC4639759 26553646
  89. Khalil AM Driscoll DJ. 2010 Epigenetic regulation of pericentromeric heterochromatin during mammalian meiosis. Cytogenet Genome Res. 129: 280– 289. 20606401 PMC3202914
  90. Kidwell MG. 2002 Transposable elements and the evolution of genome size in eukaryotes. Genetica 115: 49– 63. 12188048
  91. Koepfli K-P Paten B O’Brien SJ. 2015 The genome 10K project: a way forward. Annu Rev Anim Biosci. 3: 57– 111. 25689317 PMC5837290
  92. Koga A Iida A Hori H Shimada A Shima A. 2006 Vertebrate DNA transposon as a natural mutator: the medaka fish Tol2 element contributes to genetic variation without recognizable traces. Mol Biol Evol. 23: 1414– 1419. 16672286
  93. Koga A Wakamatsu Y Sakaizumi M Hamaguchi S Shimada A. 2009 Distribution of complete and defective copies of the Tol1 transposable element in natural populations of the medaka fish Oryzias latipes. Genes Genet Syst. 84: 345– 352. 20154421
  94. Kojima KK. 2015 A new class of SINEs with snRNA gene-derived heads. Genome Biol Evol. 7: 1702– 1712. 26019167 PMC4494074
  95. Kokošar J Kordiš D. 2013 Genesis and regulatory wiring of retroelement-derived domesticated genes: a phylogenomic perspective. Mol Biol Evol. 30: 1015– 1031. mst014. 23348003 PMC3670739
  96. Kordis D Gubensek F. 1998 Unusual horizontal transfer of a long interspersed nuclear element between distant vertebrate classes. Proc Natl Acad Sci U S A. 95: 10704– 10709. 9724768 PMC27959
  97. Kramerov D Vassetzky N. 2011 Origin and evolution of SINEs in eukaryotic genomes. Heredity (Edinb.) 107: 487– 495. 21673742 PMC3242629
  98. Krupovic M Koonin EV. 2015 Polintons: a hotbed of eukaryotic virus, transposon and plasmid evolution. Nat Rev Microbiol. 13: 105– 115. 25534808 PMC5898198
  99. Kuraku S Qiu H Meyer A. 2012 Horizontal transfers of Tc1 elements between teleost fishes and their vertebrate parasites, lampreys. Genome Biol Evol. 4: 929– 936. 22887124 PMC3516227
  100. Lander ES, 2001 Initial sequencing and analysis of the human genome. Nature 409: 860– 921. 11237011
  101. Lerat E. 2010 Identifying repeats and transposable elements in sequenced genomes: how to find your way through the dense forest of programs. Heredity (Edinb.) 104: 520– 533. 19935826
  102. Levin HL Moran JV. 2011 Dynamic interactions between transposable elements and their hosts. Nat Rev Genet. 12: 615– 627. 21850042 PMC3192332
  103. Levis RW Ganesan R Houtchens K Tolar LA Sheen F-M. 1993 Transposons in place of telomeric repeats at a Drosophila telomere. Cell 75: 1083– 1093. 8261510
  104. Lim JK Simmons MJ. 1994 Gross chromosome rearrangements mediated by transposable elements in Drosophila melanogaster. Bioessays 16: 269– 275. 8031304
  105. Lindblad-Toh K, 2011 A high-resolution map of human evolutionary constraint using 29 mammals. Nature 478: 476– 482. 21993624 PMC3207357
  106. Liu Y, 2015 Gekko japonicus genome reveals evolution of adhesive toe pads and tail regeneration. Nat Commun. 6: 1– 11. PMC4673495 26598231
  107. Locke DP, 2011 Comparative and demographic analysis of orang-utan genomes. Nature 469: 529– 533. 21270892 PMC3060778
  108. Louis A Nguyen NTT Muffato M Crollius HR. 2015 Genomicus update 2015: KaryoView and MatrixView provide a genome-wide perspective to multispecies comparative genomics. Nucleic Acids Res. 43: D682– D689. 25378326 PMC4383929
  109. Lowe CB Bejerano G Haussler D. 2007 Thousands of human mobile element fragments undergo strong purifying selection near developmental genes. Proc Natl Acad Sci U S A. 104: 8005– 8010. 17463089 PMC1876562
  110. Luan DD Korman MH Jakubczak JL Eickbush TH. 1993 Reverse transcription of R2Bm RNA is primed by a nick at the chromosomal target site: a mechanism for non-LTR retrotransposition. Cell 72: 595– 605. 7679954
  111. Lynch VJ. 2016 A copy-and-paste gene regulatory network. Science 351: 1029– 1030. 26941305
  112. Lynch VJ Leclerc RD May G Wagner GP. 2011 Transposon-mediated rewiring of gene regulatory networks contributed to the evolution of pregnancy in mammals. Nat Genet. 43: 1154– 1159. 21946353
  113. Lynch VJ, 2015 Ancient transposable elements transformed the uterine regulatory landscape and transcriptome during the evolution of mammalian pregnancy. Cell Rep. 10: 551– 561. 25640180 PMC4447085
  114. Mager DL Stoye JP. 2015 Mammalian endogenous retroviruses. Microbiol Spectrum 3: MDNA3– M0009. 26104559
  115. Matzke A, 2012 Retroposon insertion patterns of neoavian birds: strong evidence for an extensive incomplete lineage sorting era. Mol Biol Evol. 29: 1497– 1501. 22319163
  116. McGaugh SE, 2015 Rapid molecular evolution across amniotes of the IIS/TOR network. Proc Natl Acad Sci U S A. 112: 7055– 7060. 25991861 PMC4460498
  117. Metcalfe CJ Casane D. 2013 Accommodating the load: the transposable element content of very large genomes. Mob Genet Elements 3: e24775. 24616835 PMC3943481
  118. Metcalfe CJ Filée J Germon I Joss J Casane D. 2012 Evolution of the Australian lungfish (Neoceratodus forsteri) genome: a major role for CR1 and L2 LINE elements. Mol Biol Evol. 29: 3529– 3539. 22734051
  119. Michalak P. 2009 Epigenetic, transposon and small RNA determinants of hybrid dysfunctions. Heredity (Edinb.) 102: 45– 50. 18545265
  120. Mikkelsen TS, 2007 Genome of the marsupial Monodelphis domestica reveals innovation in non-coding sequences. Nature 447: 167– 177. 17495919
  121. Mills RE, 2006 Recently mobilized transposons in the human and chimpanzee genomes. Am J Hum Genet. 78: 671– 679. 16532396 PMC1424692
  122. Mitra R, 2013 Functional characterization of piggyBat from the bat Myotis lucifugus unveils an active mammalian DNA transposon. Proc Natl Acad Sci U S A. 110: 234– 239. 23248290 PMC3538221
  123. Naville M Chalopin D Casane D Laurenti P Volff J-N. 2015 The coelacanth: can a “living fossil” have active transposable elements in its genome? Mob Genet Elements 5: 55– 59. 26442185 PMC4588170
  124. Naville M Chalopin D Volff J-N. 2014 Interspecies insertion polymorphism analysis reveals recent activity of transposable elements in extant coelacanths. PLoS One 9: e114382. 25470617 PMC4255032
  125. Nellaker C, 2012 The genomic landscape shaped by selection on transposable elements across 18 mouse strains. Genome Biol. 13: R45. 22703977 PMC3446317
  126. Nikaido M, 2013 Coelacanth genomes reveal signatures for evolutionary transition from water to land. Genome Res. 23: 1740– 1748. 23878157 PMC3787270
  127. Nilsson MA. 2016 The devil is in the details: transposable element analysis of the Tasmanian devil genome. Mob Genet Elements 6: 1– 7. PMC4802805 27066301
  128. Nilsson MA Janke A Murchison EP Ning Z Hallström BM. 2012 Expansion of CORE-SINEs in the genome of the Tasmanian devil. BMC Genomics 13: 172. 22559330 PMC3403934
  129. Nishihara H Smit AF Okada N. 2006 Functional noncoding sequences derived from SINEs in the mammalian genome. Genome Res. 16: 864– 874. 16717141 PMC1484453
  130. Noonan JP McCallion AS. 2010 Genomics of long-range regulatory elements. Annu Rev Genomics Hum Genet. 11: 1– 23. 20438361
  131. Novick PA Basta H Floumanhaft M McClure MA Boissinot S. 2009 The evolutionary dynamics of autonomous non-LTR retrotransposons in the lizard Anolis carolinensis shows more similarity to fish than mammals. Mol Biol Evol. 26: 1811– 1822. 19420048
  132. Nystedt B, 2013 The Norway spruce genome sequence and conifer genome evolution. Nature 497: 579– 584. 23698360
  133. Ogiwara I Miya M Ohshima K Okada N. 1999 Retropositional parasitism of SINEs on LINEs: identification of SINEs and LINEs in elasmobranchs. Mol Biol Evol. 16: 1238– 1250. 10486979
  134. Ogiwara I Miya M Ohshima K Okada N. 2002 V-SINEs: a new superfamily of vertebrate SINEs that are widespread in vertebrate genomes and retain a strongly conserved segment within each repetitive unit. Genome Res. 12: 316– 324. 11827951 PMC155270
  135. Ohshima K Okada N. 2005 SINEs and LINEs: symbionts of eukaryotic genomes with a common tail. Cytogenet Genome Res. 110: 475– 490. 16093701
  136. Oliver KR Greene WK. 2011 Mobile DNA and the TE-Thrust hypothesis: supporting evidence from the primates. Mob DNA 2: 8 21627776 PMC3123540
  137. Oliver KR Greene WK. 2012 Transposable elements and viruses as factors in adaptation and evolution: an expansion and strengthening of the TE‐Thrust hypothesis. Ecol Evol. 2: 2912– 2933. 23170223 PMC3501640
  138. Oliver KR Greene WK. 2009 Transposable elements: powerful facilitators of evolution. Bioessays 31: 703– 714. 19415638
  139. Orgel LE Crick FH. 1980 Selfish DNA: the ultimate parasite. Nature 284: 604– 607. 7366731
  140. Pace JK Feschotte C. 2007 The evolutionary history of human DNA transposons: evidence for intense activity in the primate lineage. Genome Res. 17: 422– 432. 17339369 PMC1832089
  141. Pagán HJ, 2012 Survey sequencing reveals elevated DNA transposon activity, novel elements, and variation in repetitive landscapes among vesper bats. Genome Biol Evol. 4: 575– 585. 22491057 PMC3342881
  142. Pagan HJ Smith JD Hubley RM Ray DA. 2010 PiggyBacing on a primate genome: novel elements, recent activity and horizontal transfer. Genome Biol Evol. 2: 293– 303. 20624734 PMC2997546
  143. Pask AJ, 2009 Analysis of the platypus genome suggests a transposon origin for mammalian imprinting. Genome Biol. 10: R1. 19121219 PMC2687786
  144. Piégu B Bire S Arensburger P Bigot Y. 2015 A survey of transposable element classification systems–a call for a fundamental update to meet the challenge of their diversity and complexity. Mol Phylogenet Evol. 86: 90– 109. 25797922
  145. Platt RN Blanco-Berdugo L Ray DA. 2016 Accurate transposable element annotation is vital when analyzing new genome assemblies. Genome Biol Evol. evw009. PMC4779615 26802115
  146. Platt RN, 2014 Large numbers of novel miRNAs originate from DNA transposons and are coincident with a large species radiation in bats. Mol Biol Evol. 31: 1536– 1545. 24692655
  147. Platt RN Ray DA. 2012 A non-LTR retroelement extinction in Spermophilus tridecemlineatus. Gene 500: 47– 53. 22465530
  148. Platt RN Mangum SF Ray DA. 2016 Pinpointing the vesper bat transposon revolution using the Miniopterus natalensis genome. Mob DNA 7: 12. 27489570 PMC4971623
  149. Poelstra JW, 2014 The genomic landscape underlying phenotypic integrity in the face of gene flow in crows. Science 344: 1410– 1414. 24948738
  150. Pop M. 2009 Genome assembly reborn: recent computational challenges. Brief Bioinform. 10: 354– 366. 19482960 PMC2691937
  151. Poulet FM Bowser PR Casey JW. 1994 Retroviruses of fish, reptiles, and molluscs In: Levy J, editor. The retroviridae. New York (NY): Springer p. 1– 38.
  152. Poulter R Butler M. 1998 A retrotransposon family from the pufferfish (fugu) Fugu rubripes. Gene 215: 241– 249. 9714821
  153. Pritham EJ Feschotte C. 2007 Massive amplification of rolling-circle transposons in the lineage of the bat Myotis lucifugus. Proc Natl Acad Sci U S A. 104: 1895– 1900. 17261799 PMC1794268
  154. Pritham EJ Putliwala T Feschotte C. 2007 Mavericks, a novel class of giant transposable elements widespread in eukaryotes and related to DNA viruses. Gene 390: 3– 17. 17034960
  155. Ray DA Batzer MA. 2005 Tracking Alu evolution in New World primates. BMC Evol Biol. 5: 51. 16209711 PMC1266357
  156. Ray DA, 2008 Multiple waves of recent DNA transposon activity in the bat, Myotis lucifugus. Genome Res. 18: 717– 728. 18340040 PMC2336803
  157. Ray DA, 2015 Differential SINE evolution in vesper and non-vesper bats. Mobile DNA 6: 1–10. PMC4436864 25991928
  158. Ray DA Pagan HJ Thompson ML Stevens RD. 2007 Bats with hATs: evidence for recent DNA transposon activity in genus Myotis. Mol Biol Evol. 24: 632– 639. 17150974
  159. Rebollo R Romanish MT Mager DL. 2012 Transposable elements: an abundant and natural source of regulatory sequences for host genes. Annu Rev Genet. 46: 21– 42. 22905872
  160. Renfree MB, 2011 Genome sequence of an Australian kangaroo, Macropus eugenii, provides insight into the evolution of mammalian reproduction and development. Genome Biol. 12: R81. 21854559 PMC3277949
  161. Rinehart T Grahn R Wichman H. 2005 SINE extinction preceded LINE extinction in sigmodontine rodents: implications for retrotranspositional dynamics and mechanisms. Cytogenet Genome Res. 110: 416– 425. 16093694
  162. Sasaki T, 2008 Possible involvement of SINEs in mammalian-specific brain formation. Proc Natl Acad Sci U S A. 105: 4220– 4225. 18334644 PMC2393765
  163. Schaack S Gilbert C Feschotte C. 2010 Promiscuous DNA: horizontal transfer of transposable elements and why it matters for eukaryotic evolution. Trends Ecol Evol. 25: 537– 546. 20591532 PMC2940939
  164. Schmidt D, 2012 Waves of retrotransposon expansion remodel genome organization and CTCF binding in multiple mammalian lineages. Cell 148: 335– 348. 22244452 PMC3368268
  165. Schmitz J, 2008 Retroposed SNOfall—a mammalian-wide comparison of platypus snoRNAs. Genome Res. 18: 1005– 1010. 18463303 PMC2413151
  166. Shaffer HB, 2013 The western painted turtle genome, a model for the evolution of extreme physiological adaptations in a slowly evolving lineage. Genome Biol. 14: R28. 23537068 PMC4054807
  167. Shen C-H Steiner LA. 2004 Genome structure and thymic expression of an endogenous retrovirus in zebrafish. J Virol. 78: 899– 911. 14694121 PMC368747
  168. Shimamura M Abe H Nikaido M Ohshima K Okada N. 1999 Genealogy of families of SINEs in cetaceans and artiodactyls: the presence of a huge superfamily of tRNA (Glu)-derived families of SINEs. Mol Biol Evol. 16: 1046– 1060. 10474901
  169. Siguier P Gourbeyre E Varani A Ton-Hoang B Chandler M. 2015 Everyman's guide to bacterial insertion sequences. Microbiol Spectrum 3: MDNA3-0030-2014. 26104715
  170. Silva JC Loreto EL Clark JB. 2004 Factors that affect the horizontal transfer of transposable elements. Curr Issues Mol Biol. 6: 57– 71. 14632259
  171. Smeds L, 2015 Evolutionary analysis of the female-specific avian W chromosome. Nat Commun. 6: 7330 PMC4468903 26040272
  172. Smith JJ Antonacci F Eichler EE Amemiya CT. 2009 Programmed loss of millions of base pairs from a vertebrate genome. Proc Natl Acad Sci U S A. 106: 11212– 11217. 19561299 PMC2708698
  173. Smith JJ, 2013 Sequencing of the sea lamprey (Petromyzon marinus) genome provides insights into vertebrate evolution. Nat Genet. 45: 415– 421. 23435085 PMC3709584
  174. Smith JJ Sumiyama K Amemiya CT. 2012 A living fossil in the genome of a living fossil: Harbinger transposons in the coelacanth genome. Mol Biol Evol. 29: 985– 993. 22045999 PMC3278475
  175. Song B, 2015 A genome draft of the legless anguid lizard, Ophisaurus gracilis. DNA 56:3.19. PMC4391233 25859342
  176. St John J Quinn TW. 2008 Identification of novel CR1 subfamilies in an avian order with recently active elements. Mol Phylogenet Evol. 49: 1008– 1014. 18929670
  177. Stapley J Santure AW Dennis SR. 2015 Transposable elements as agents of rapid adaptation may explain the genetic paradox of invasive species. Mol Ecol. 24: 2241– 2252. 25611725
  178. Suh A. 2015 The specific requirements for CR1 retrotransposition explain the scarcity of retrogenes in birds. J Mol Evol. 81: 18– 20. 26223967
  179. Suh A, 2015 Multiple lineages of ancient CR1 retroposons shaped the early genome evolution of amniotes. Genome Biol Evol. 7: 205– 217. PMC4316615 25503085
  180. Suh A Kriegs JO Brosius J Schmitz J. 2011 Retroposon insertions and the chronology of avian sex chromosome evolution. Mol Biol Evol. 28: 2993– 2997. 21633113
  181. Suh A Kriegs JO Donnellan S Brosius J Schmitz J. 2012 A universal method for the study of CR1 retroposons in nonmodel bird genomes. Mol Biol Evol. 29: 2899– 2903. 22522308
  182. Suh A, 2011 Mesozoic retroposons reveal parrots as the closest living relatives of passerine birds. Nat Commun. 2: 443. 21863010 PMC3265382
  183. Suh A Smeds L Ellegren H. 2015 The dynamics of incomplete lineage sorting across the ancient adaptive radiation of neoavian birds. PLoS Biol. 13: e1002224. 26284513 PMC4540587
  184. Suh A, 2014 Early Mesozoic coexistence of amniotes and Hepadnaviridae. PLoS Genet. 10: e1004559. 25501991 PMC4263362
  185. Suh A, 2016 Ancient horizontal transfers of retrotransposons between birds and ancestors of human pathogenic nematodes. Nat Commun. 7: 11396. 27097561 PMC4844689
  186. Sun C Arriaza JRL Mueller RL. 2012 Slow DNA loss in the gigantic genomes of salamanders. Genome Biol Evol. 4: 1340– 1348. 23175715 PMC3542557
  187. Sun C, 2012 LTR retrotransposons contribute to genomic gigantism in plethodontid salamanders. Genome Biol Evol. 4: 168– 183. 22200636 PMC3318908
  188. Sun Y-B, 2015 Whole-genome sequence of the Tibetan frog Nanorana parkeri and the comparative evolution of tetrapod genomes. Proc Natl Acad Sci U S A. 112: E1257– E1262. 25733869 PMC4371989
  189. Terai Y Takahashi K Okada N. 1998 SINE cousins: the 3'-end tails of the two oldest and distantly related families of SINEs are descended from the 3'ends of LINEs with the same genealogical origin. Mol Biol Evol. 15: 1460– 1471. 12572609
  190. Thomas J Phillips CD Baker RJ Pritham EJ. 2014 Rolling-circle transposons catalyze genomic innovation in a mammalian lineage. Genome Biol Evol. 6: 2595– 2610. 25223768 PMC4224331
  191. Thomas J Schaack S Pritham EJ. 2010 Pervasive horizontal transfer of rolling-circle transposons among animals. Genome Biol Evol. 2: 656– 664. 20693155 PMC2997563
  192. Tollis M Boissinot S. 2013 Lizards and LINEs: selection and demography affect the fate of L1 retrotransposons in the genome of the green anole (Anolis carolinensis). Genome Biol Evol. 5: 1754– 1768. 24013105 PMC3787681
  193. Tsutsumi M, 2006 Color reversion of the albino medaka fish associated with spontaneous somatic excision of the Tol‐1 transposable element from the tyrosinase gene. Pigment Cell Res. 19: 243– 247. 16704459
  194. Van de Lagemaat LN Landry J-R Mager DL Medstrand P. 2003 Transposable elements in mammals promote regulatory variation and diversification of genes with specialized functions. Trends Genet. 19: 530– 536. 14550626
  195. Vassetzky NS Kramerov DA. 2013 SINEBase: a database and tool for SINE analysis. Nucleic Acids Res. 41: D83– D89. 23203982 PMC3531059
  196. Venkatesh B, 2007 Survey sequencing and comparative analysis of the elephant shark (Callorhinchus milii) genome. PLoS Biol. 5: e101. 17407382 PMC1845163
  197. Venkatesh B, 2014 Elephant shark genome provides unique insights into gnathostome evolution. Nature 505: 174– 179. 24402279 PMC3964593
  198. Venkatesh B Tay A Dandona N Patil JG Brenner S. 2005 A compact cartilaginous fish model genome. Curr Biol. 15: R82– R83. 15694293
  199. Ventura M, 2011 Gorilla genome structural variation reveals evolutionary parallelisms with chimpanzee. Genome Res. 21: 1640– 1649. 21685127 PMC3202281
  200. Vijay N, 2016 Evolution of heterogeneous genome differentiation across multiple contact zones in a crow species complex. Nat Commun. 7: 13195. 27796282 PMC5095515

200 of 220 shown

Cited by

Sorted by citations

Authors
Sotero-Caio, C. G., Platt, R. N., Suh, A., & Ray, D. A.
Affiliations
  • Texas Tech University (US)
  • Uppsala University (SE)
Corresponding author
Ray, David A.
ORCID
Venue
Genome Biology and Evolution
Publisher
Oxford University Press (OUP)
Published
2017-01
Volume
9
Issue
1
Pages
161-177
ISSN
1759-6653 (ISSN-L)
DOI
10.1093/gbe/evw264
PMC
PMC5381603
OpenAlex
W2584829257
Cited by
283
References
7
Citations by year
2026: 33 · 2025: 17 · 2024: 31 · 2023: 30 · 2022: 34 · 2021: 38 · 2020: 41 · 2019: 32 · 2018: 16 · 2017: 8 · 2012: 1
FWCI
1.78
Type
journal article
Language
en
Open access
Locations
  • Genome Biology and Evolution (publishedVersion)
  • PubMed Central (publishedVersion, cc-by-nc)
  • PubMed (publishedVersion)
  • KTH Publication Database DiVA (KTH Royal Institute of Technology) (submittedVersion, other-oa)
  • ThinkTech (Texas Tech University) (submittedVersion, cc-by-nc)
  • UEA Digital Repository (University of East Anglia) (submittedVersion)
Funders
  • National Science Foundation
  • Francis Crick Institute
Topics
  • Life Sciences › Agricultural and Biological Sciences › Plant Science › Chromosomal and Genetic Variations
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genome Rearrangement Algorithms
Keywords
transposable elements, vertebrate genomes, retrotransposition, transposition, TE annotation, genome assembly, long-read sequencing, Actinopterygii, amphibians, birds and mammals
MeSH terms
Animals, DNA Transposable Elements, Biological Evolution, Phylogeny, Vertebrates, Sequence Analysis, DNA

About these checks

Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

Statistics and arithmetic are recomputed, not judged.

Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.

What counts as a claim ›How we measure confidence ›How we check this ›

Are you an author, or do you see a problem with this page? Request a review