Journal Mobile Options
Table of Contents
Vol. 140, No. 2-4, 2013
Issue release date: July 2013
Section title: Retrotransposons in Hybrids and Allopolyploid Genomes
Cytogenet Genome Res 2013;140:295-311
(DOI:10.1159/000352069)

Genetic and Epigenetic Changes Involving (Retro)transposons in Animal Hybrids and Polyploids

Arkhipova I.R. · Rodriguez F.
Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, Mass., USA

Do you have an account?

Register and profit from personalized services (MyKarger) Login Information

Please create your User ID & Password





Contact Information









I have read the Karger Terms and Conditions and agree.

Register and profit from personalized services (MyKarger) Login Information

Please create your User ID & Password





Contact Information









I have read the Karger Terms and Conditions and agree.

To view the fulltext, please log in

To view the pdf, please log in

Buy

  • FullText & PDF
  • Unlimited re-access via MyKarger (new!)
  • Unrestricted printing, no saving restrictions for personal use
  • Reduced rates with a PPV account
read more

Direct: USD 38.00
Account: USD 26.50

Select

Rent/Cloud

  • Rent for 48h to view
  • Buy Cloud Access for unlimited viewing via different devices
  • Synchronizing in the ReadCube Cloud
  • Printing and saving restriction apply

Rental: USD 8.50
Cloud: USD 20.00

Select

Subscribe

  • Automatic perpetual access to all articles of the subscribed year(s)
  • Unlimited re-access via Subscriber Login or MyKarger
  • Unrestricted printing, no saving restrictions for personal use
read more

Subcription rates


Select


Article / Publication Details

First-Page Preview
Abstract of Retrotransposons in Hybrids and Allopolyploid Genomes

Published online: 7/8/2013

Number of Print Pages: 17
Number of Figures: 2
Number of Tables: 0

ISSN: 1424-8581 (Print)
eISSN: 1424-859X (Online)

For additional information: http://www.karger.com/CGR

Abstract

Transposable elements (TEs) are discrete genetic units that have the ability to change their location within chromosomal DNA, and constitute a major and rapidly evolving component of eukaryotic genomes. They can be subdivided into 2 distinct types: retrotransposons, which use an RNA intermediate for transposition, and DNA transposons, which move only as DNA. Rapid advances in genome sequencing significantly improved our understanding of TE roles in genome shaping and restructuring, and studies of transcriptomes and epigenomes shed light on the previously unknown molecular mechanisms underlying genetic and epigenetic TE controls. Knowledge of these control systems may be important for better understanding of reticulate evolution and speciation in the context of bringing different genomes together by hybridization and perturbing the established regulatory balance by ploidy changes. See also sister article focusing on plants by Bento et al. in this themed issue.


Article / Publication Details

First-Page Preview
Abstract of Retrotransposons in Hybrids and Allopolyploid Genomes

Published online: 7/8/2013

Number of Print Pages: 17
Number of Figures: 2
Number of Tables: 0

ISSN: 1424-8581 (Print)
eISSN: 1424-859X (Online)

For additional information: http://www.karger.com/CGR


Copyright / Drug Dosage

Copyright: All rights reserved. No part of this publication may be translated into other languages, reproduced or utilized in any form or by any means, electronic or mechanical, including photocopying, recording, microcopying, or by any information storage and retrieval system, without permission in writing from the publisher or, in the case of photocopying, direct payment of a specified fee to the Copyright Clearance Center.
Drug Dosage: The authors and the publisher have exerted every effort to ensure that drug selection and dosage set forth in this text are in accord with current recommendations and practice at the time of publication. However, in view of ongoing research, changes in goverment regulations, and the constant flow of information relating to drug therapy and drug reactions, the reader is urged to check the package insert for each drug for any changes in indications and dosage and for added warnings and precautions. This is particularly important when the recommended agent is a new and/or infrequently employed drug.
Disclaimer: The statements, opinions and data contained in this publication are solely those of the individual authors and contributors and not of the publishers and the editor(s). The appearance of advertisements or/and product references in the publication is not a warranty, endorsement, or approval of the products or services advertised or of their effectiveness, quality or safety. The publisher and the editor(s) disclaim responsibility for any injury to persons or property resulting from any ideas, methods, instructions or products referred to in the content or advertisements.

References

  1. Albertin W, Marullo P: Polyploidy in fungi: evolution after whole-genome duplication. Proc Biol Sci 279:2497-2509 (2012).
  2. Alföldi J, Di Palma F, Grabherr M, Williams C, Kong L, et al: The genome of the green anole lizard and a comparative analysis with birds and mammals. Nature 477:587-591 (2011).
  3. Aravin AA, Gaidatzis D, Pfeffer S, Lagos-Quintana M, Landgraf P, et al: A novel class of small RNAs bind to MILI protein in mouse testes. Nature 442:203-207 (2006).
  4. Aravin AA, Hannon GJ, Brennecke J: The Piwi-piRNA pathway provides an adaptive defense in the transposon arms race. Science 318:761-764 (2007a).
  5. Aravin AA, Sachidanandam R, Girard A, Fejes-Toth K, Hannon GJ: Developmentally regulated piRNA clusters implicate MILI in transposon control. Science 316:744-747 (2007b).
  6. Arkhipova IR: Distribution and phylogeny of Penelope-like elements in eukaryotes. Syst Biol 55:875-885 (2006).
  7. Arkhipova I, Meselson M: Deleterious transposable elements and the extinction of asexuals. Bioessays 27:76-85 (2005).
  8. Armisen J, Gilchrist MJ, Wilczynska A, Standart N, Miska EA: Abundant and dynamically expressed miRNAs, piRNAs, and other small RNAs in the vertebrate Xenopus tropicalis. Genome Res 19:1766-1775 (2009).
  9. Arnaiz O, Goût JF, Bétermier M, Bouhouche K, Cohen J, et al: Gene expression in a paleopolyploid: a transcriptome resource for the ciliate Paramecium tetraurelia. BMC Genomics 11:547 (2010).
  10. Ashe A, Sapetschnig A, Weick EM, Mitchell J, Bagijn MP, et al: piRNAs can trigger a multigenerational epigenetic memory in the germline of C. elegans. Cell 150:88-99 (2012).
  11. Aury JM, Jaillon O, Duret L, Noel B, Jubin C, et al: Global trends of whole-genome duplications revealed by the ciliate Paramecium tetraurelia. Nature 444:171-178 (2006).
  12. Avise JC: Clonality: the Genetics, Ecology, and Evolution of Sexual Abstinence in Vertebrate Animals (Oxford University Press, Oxford 2008).
  13. Bernardi G, Wiley EO, Mansour H, Miller MR, Orti G, et al: The fishes of Genome 10K. Mar Genomics 7:3-6 (2012).
  14. Bi K, Bogart JP: Probing the meiotic mechanism of intergenomic exchanges by genomic in situ hybridization on lampbrush chromosomes of unisexual Ambystoma (Amphibia: Caudata). Chromosome Res 18:371-382 (2010).
  15. Bingham PM, Kidwell MG, Rubin GM: The molecular basis of P-M hybrid dysgenesis: the role of the P element, a P-strain-specific transposon family. Cell 29:995-1004 (1982).
  16. Bird A, Tate P, Nan X, Campoy J, Meehan R, et al: Studies of DNA methylation in animals. J Cell Sci Suppl 19:37-39 (1995).

    External Resources

  17. Blackman RK, Grimaila R, Koehler MM, Gelbart WM: Mobilization of hobo elements residing within the decapentaplegic gene complex: suggestion of a new hybrid dysgenesis system in Drosophila melanogaster. Cell 49:497-505 (1987).
  18. Blumenstiel JP, Hartl DL: Evidence for maternally transmitted small interfering RNA in the repression of transposition in Drosophila virilis. Proc Natl Acad Sci USA 102:15965-15970 (2005).
  19. Bouhouche K, Gout JF, Kapusta A, Bétermier M, Meyer E: Functional specialization of Piwi proteins in Paramecium tetraurelia from post-transcriptional gene silencing to genome remodelling. Nucleic Acids Res 39:4249-4264 (2011).
  20. Brennecke J, Aravin AA, Stark A, Dus M, Kellis M, et al: Discrete small RNA-generating loci as master regulators of transposon activity in Drosophila. Cell 128:1089-1103 (2007).
  21. Brennecke J, Malone CD, Aravin AA, Sachidanandam R, Stark A, Hannon GJ: An epigenetic role for maternally inherited piRNAs in transposon silencing. Science 322:1387-1392 (2008).
  22. Brown JD, O'Neill RJ: Chromosomes, conflict, and epigenetics: chromosomal speciation revisited. Annu Rev Genomics Hum Genet 11:291-316 (2010).
  23. Brown JD, Golden D, O'Neill RJ: Methylation perturbations in retroelements within the genome of a Mus interspecific hybrid correlate with double minute chromosome formation. Genomics 91:267-273 (2008).
  24. Brown JD, Piccuillo V, O'Neill RJ: Retroelement demethylation associated with abnormal placentation in Mus musculus × Mus caroli hybrids. Biol Reprod 86:88 (2012).
  25. Bucheton A, Paro R, Sang HM, Pelisson A, Finnegan DJ: The molecular basis of I-R hybrid dysgenesis in Drosophila melanogaster: identification, cloning, and properties of the I factor. Cell 38:153-163 (1984).
  26. Burki E: The expression of creatine kinase isozymes in Xenopus tropicalis, Xenopus laevis laevis, and their viable hybrid. Biochem Genet 23:73-88 (1985).
  27. Cáceres M, Ranz JM, Barbadilla A, Long M, Ruiz A: Generation of a widespread Drosophila inversion by a transposable element. Science 285:415-418 (1999).
  28. Cantu D, Vanzetti LS, Sumner A, Dubcovsky M, Matvienko M, et al: Small RNAs, DNA methylation and transposable elements in wheat. BMC Genomics 11:408 (2010).
  29. Carbone L, Harris RA, Vessere GM, Mootnick AR, Humphray S, et al: Evolutionary breakpoints in the gibbon suggest association between cytosine methylation and karyotype evolution. PLoS Genet 5:e1000538 (2009).
  30. Carbone L, Harris RA, Mootnick AR, Milosavljevic A, Martin DIK, et al: Centromere remodeling in Hoolock leuconedys (Hylobatidae) by a new transposable element unique to the gibbons. Genome Biol Evol 4:648-658 (2012).
  31. Carmi S, Church GM, Levanon EY: Large-scale DNA editing of retrotransposons accelerates mammalian genome evolution. Nat Commun 2:519 (2011).
  32. Casals F, Cáceres M, Manfrin MH, González J, Ruiz A: Molecular characterization and chromosomal distribution of Galileo, Kepler and Newton, three foldback transposable elements of the Drosophila buzzatii species complex. Genetics 169:2047-2059 (2005).
  33. Castoe TA, Hall KT, Guibotsy Mboulas ML, Gu W, de Koning AP, et al: Discovery of highly divergent repeat landscapes in snake genomes using high-throughput sequencing. Genome Biol Evol 3:641-653 (2011).
  34. Chambeyron S, Popkova A, Payen-Groschene G, Brun C, Laouini D, et al: piRNA-mediated nuclear accumulation of retrotransposon transcripts in the Drosophila female germline. Proc Natl Acad Sci USA 105:14964-14969 (2008).
  35. Charlesworth B, Sniegowski P, Stephan W: The evolutionary dynamics of repetitive DNA in eukaryotes. Nature 371:215-220 (1994).
  36. Chen Y, Pane A, Schupbach T: Cutoff and Aubergine mutations result in retrotransposon upregulation and checkpoint activation in Drosophila. Curr Biol 17:637-642 (2007).
  37. Chiu YL, Greene WC: The APOBEC3 cytidine deaminases: an innate defensive network opposing exogenous retroviruses and endogenous retroelements. Annu Rev Immunol 26:317-353 (2008).
  38. Colbourne JK, Pfrender ME, Gilbert D, Thomas WK, Tucker A, et al: The ecoresponsive genome of Daphnia pulex. Science 331:555-561 (2011).
  39. Cox DN, Chao A, Baker J, Chang L, Qiao D, Lin H: A novel class of evolutionarily conserved genes defined by piwi are essential for stem cell self-renewal. Genes Dev 12:3715-3727 (1998).
  40. Cunningham C, Mootnick A: Gibbons. Curr Biol 19:R543-R544 (2009).
  41. Czech B, Malone CD, Zhou R, Stark A, Schlingeheyde C, et al: An endogenous small interfering RNA pathway in Drosophila. Nature 453:798-802 (2008).
  42. Das PP, Bagijn MP, Goldstein LD, Woolford JR, Lehrbach NJ, et al: Piwi and piRNAs act upstream of an endogenous siRNA pathway to suppress Tc3 transposon mobility in the Caenorhabditis elegans germline. Mol Cell 31:79-90 (2008).
  43. Davidson WS, Koop BF, Jones SJ, Iturra P, Vidal R, et al: Sequencing the genome of the Atlantic salmon (Salmo salar). Genome Biol 11:403 (2010).

    External Resources

  44. de Boer JG, Yazawa R, Davidson WS, Koop BF: Bursts and horizontal evolution of DNA transposons in the speciation of pseudotetraploid salmonids. BMC Genomics 8:422 (2007).
  45. Delprat A, Negre B, Puig M, Ruiz A: The transposon Galileo generates natural chromosomal inversions in Drosophila by ectopic recombination. PLoS One 4:e7883 (2009).
  46. Desset S, Meignin C, Dastugue B, Vaury C: COM, a heterochromatic locus governing the control of independent endogenous retroviruses from Drosophila melanogaster. Genetics 164:501-509 (2003).

    External Resources

  47. Eickbush TH, Malik HS: Origin and evolution of retrotransposons, in Craig NL, Craigie R, Gellert M, Lambowitz AM (eds): Mobile DNA II, pp 1111-1144 (ASM Press, Washington 2002).
  48. Evans BJ: Genome evolution and speciation genetics of clawed frogs (Xenopus and Silurana). Front Biosci 13:4687-4706 (2008).
  49. Evgen'ev MB, Arkhipova IR: Penelope-like elements - a new class of retroelements: distribution, function, and possible evolutionary significance. Cytogenet Genome Res 110:510-521 (2005).
  50. Evgen'ev MB, Zelentsova H, Shostak N, Kozitsina M, Barskyi V, et al: Penelope, a new family of transposable elements and its possible role in hybrid dysgenesis in Drosophila virilis. Proc Natl Acad Sci USA 94:196-201 (1997).
  51. Evgen'ev MB, Zelentsova H, Poluectova H, Lyozin GT, Veleikodvorskaja V, et al: Mobile elements and chromosomal evolution in the virilis group of Drosophila. Proc Natl Acad Sci USA 97:11337-11342 (2000).
  52. Fang W, Wang X, Bracht JR, Nowacki M, Landweber LF: Piwi-interacting RNAs protect DNA against loss during Oxytricha genome rearrangement. Cell 151:1243-1255 (2012).
  53. Faunes F, Almonacid LI, Melo F, Larrain J: Characterization of small RNAs in Xenopus tropicalis gastrulae. Genesis 50:572-583 (2012).
  54. Fedoroff NV: Transposable elements, epigenetics, and genome evolution. Science 338:758-767 (2012).
  55. Feldman M, Levy AA: Genome evolution due to allopolyploidization in wheat. Genetics 192:763-774 (2012).
  56. Ferreri GC, Brown JD, Obergfell C, Jue N, Finn CE, et al: Recent amplification of the kangaroo endogenous retrovirus, KERV, limited to the centromere. J Virol 85:4761-4771 (2011).
  57. Feschotte C, Pritham EJ: DNA transposons and the evolution of eukaryotic genomes. Annu Rev Genet 41:331-368 (2007).
  58. Flot JF, Hespeels B, Li X, Noel B, Arkhipova I, et al: Genomic evidence for ameiotic evolution in the bdelloid rotifer Adineta vaga. Nature, in press (2013).
  59. Fontdevila A: Hybrid genome evolution by transposition. Cytogenet Genome Res 110:49-55 (2005).
  60. Gallardo MH, González CA, Cebrián I: Molecular cytogenetics and allotetraploidy in the red vizcacha rat, Tympanoctomys barrerae (Rodentia, Octodontidae). Genomics 88:214-221 (2006).
  61. Genome 10K Community of Scientists: Genome 10K: a proposal to obtain whole-genome sequence for 10,000 vertebrate species. J Hered 100:659-674 (2009).
  62. Ghildiyal M, Zamore PD: Small silencing RNAs: an expanding universe. Nat Rev Genet 10:94-108 (2009).
  63. Ghildiyal M, Seitz H, Horwich MD, Li C, Du T, et al: Endogenous siRNAs derived from transposons and mRNAs in Drosophila somatic cells. Science 320:1077-1081 (2008).
  64. Girard A, Hannon GJ: Conserved themes in small-RNA-mediated transposon control. Trends Cell Biol 18:136-148 (2008).
  65. Girard A, Sachidanandam R, Hannon GJ, Carmell MA: A germline-specific class of small RNAs binds mammalian Piwi proteins. Nature 442:199-202 (2006).
  66. Gladyshev EA, Arkhipova IR: Telomere-associated endonuclease-deficient Penelope-like retroelements in diverse eukaryotes. Proc Natl Acad Sci USA 104:9352-9357 (2007).
  67. Gladyshev EA, Arkhipova IR: A single-copy IS5-like transposon in the genome of the bdelloid rotifer Adineta vaga. Mol Biol Evol 26:1921-1929 (2009a).
  68. Gladyshev EA, Arkhipova IR: Rotifer rDNA-specific R9 retrotransposable elements generate an exceptionally long target site duplication upon insertion. Gene 448:145-150 (2009b).
  69. Gladyshev EA, Arkhipova IR: A subtelomeric non-LTR retrotransposon Hebe in the bdelloid rotifer Adineta vaga is subject to inactivation by deletions but not 5′ truncations. Mob DNA 1:12 (2010a).
  70. Gladyshev EA, Arkhipova IR: Genome structure of bdelloid rotifers: shaped by asexuality or desiccation? J Hered 101:S85-S93 (2010b).
  71. Gladyshev E, Meselson M: Extreme resistance of bdelloid rotifers to ionizing radiation. Proc Natl Acad Sci USA 105:5139-5144 (2008).
  72. Gladyshev EA, Meselson M, Arkhipova IR: A deep-branching clade of retrovirus-like retrotransposons in bdelloid rotifers. Gene 390:136-145 (2007).
  73. Gladyshev EA, Meselson M, Arkhipova IR: Massive horizontal gene transfer in bdelloid rotifers. Science 320:1210-1213 (2008).
  74. Gray YH: It takes two transposons to tango: transposable-element-mediated chromosomal rearrangements. Trends Genet 16:461-468 (2000).
  75. Gregory TR: Animal genome size database. http://www.genomesize.com (2012).
  76. Grimson A, Srivastava M, Fahey B, Woodcroft BJ, Chiang HR, et al: Early origins and evolution of microRNAs and Piwi-interacting RNAs in animals. Nature 455:1193-1197 (2008).
  77. Grivna ST, Beyret E, Wang Z, Lin H: A novel class of small RNAs in mouse spermatogenic cells. Genes Dev 20:1709-1714 (2006).
  78. Gutierrez A, Sommer RJ: Evolution of dnmt-2 and mbd-2-like genes in the free-living nematodes Pristionchus pacificus, Caenorhabditis elegans and Caenorhabditis briggsae. Nucleic Acids Res 32:6388-6396 (2004).
  79. Ha M, Lu J, Tian L, Ramachandran V, Kasschau KD, et al: Small RNAs serve as a genetic buffer against genomic shock in Arabidopsis interspecific hybrids and allopolyploids. Proc Natl Acad Sci USA 106:17835-17840 (2009).
  80. Hägele K, Oschmann B: Non-reciprocal gonadal dysgenesis in hybrids of the chironomid midge Chironomus thummi. III. Germ line specific abnormalities. Chromosoma 96:50-54 (1987).
  81. Han JS: Non-long terminal repeat (non-LTR) retrotransposons: mechanisms, recent developments, and unanswered questions. Mob DNA 1:15 (2010).
  82. Hartl DL, Lohe AR, Lozovskaya ER: Modern thoughts on an ancyent marinere: function, evolution, regulation. Annu Rev Genet 31:337-358 (1997).
  83. Havecker ER, Gao X, Voytas DF: The diversity of LTR retrotransposons. Genome Biol 5:225 (2004).
  84. Hellsten U, Khokha MK, Grammer TC, Harland RM, Richardson P, Rokhsar DS: Accelerated gene evolution and subfunctionalization in the pseudotetraploid frog Xenopus laevis. BMC Biol 5:31 (2007).
  85. Hellsten U, Harland RM, Gilchrist MJ, Hendrix D, Jurka J, et al: The genome of the Western clawed frog Xenopus tropicalis. Science 328:633-636 (2010).
  86. Hickey DA: Selfish DNA: a sexually-transmitted nuclear parasite. Genetics 101:519-531 (1982).

    External Resources

  87. Houwing S, Berezikov E, Ketting RF: Zili is required for germ cell differentiation and meiosis in zebrafish. EMBO J 27:2702-2711 (2008).
  88. Hur JH, Van Doninck K, Mandigo ML, Meselson M: Degenerate tetraploidy was established before bdelloid rotifer families diverged. Mol Biol Evol 26:375-383 (2009).
  89. Inácio A, Pinho J, Pereira PM, Comai L, Coelho MM: Global analysis of the small RNA transcriptome in different ploidies and genomic combinations of a vertebrate complex - the Squalius alburnoides. PLoS One 7:e41158 (2012).
  90. International Human Genome Sequencing Consortium: Human genome. Nature 409:860-921 (2001).
  91. Jaillon O, Aury JM, Wincker P: ‘Changing by doubling', the impact of whole genome duplications in the evolution of eukaryotes. C R Biol 332:241-253 (2009).
  92. James-Zorn C, Ponferrada VG, Jarabek CJ, Burns KA, Segerdell EJ, et al: Xenbase: expansion and updates of the Xenopus model organism database. Nucleic Acids Res 41:D865-D870 (2013).
  93. Janes DE, Organ CL, Fujita MK, Shedlock AM, Edwards SV: Genome evolution in Reptilia, the sister group of mammals. Annu Rev Genomics Hum Genet 11:239-264 (2010).
  94. Juliano C, Wang J, Lin H: Uniting germline and stem cells: the function of Piwi proteins and the piRNA pathway in diverse organisms. Annu Rev Genet 45:447-469 (2011).
  95. Jurka J, Kapitonov VV, Kohany O, Jurka MV: Repetitive sequences in complex genomes: structure and evolution. Annu Rev Genomics Hum Genet 8:241-259 (2007).
  96. Kapitonov VV, Jurka J: Molecular paleontology of transposable elements in the Drosophila melanogaster genome. Proc Natl Acad Sci USA 100:6569-6574 (2003).
  97. Kapitonov VV, Jurka J: Self-synthesizing DNA transposons in eukaryotes. Proc Natl Acad Sci USA 103:4540-4545 (2006).
  98. Kapitonov VV, Jurka J: Helitrons on a roll: eukaryotic rolling-circle transposons. Trends Genet 23:521-529 (2007).
  99. Kapitonov VV, Jurka J: A universal classification of eukaryotic transposable elements implemented in Repbase. Nat Rev Genet 9:411-412 (2008).
  100. Kazazian HH Jr: Mobile elements: drivers of genome evolution. Science 303:1626-1632 (2004).
  101. Kearney M, Fujita MK, Ridenour J: Lost sex in the reptiles: constraints and correlations, in Schön I, Martens K, van Dijk P (eds): Lost Sex, pp 447-474 (Springer, Berlin 2009).

    External Resources

  102. Kelleher ES, Edelman NB, Barbash DA: Drosophila interspecific hybrids phenocopy piRNA-pathway mutants. PLoS Biol 10:e1001428 (2012).
  103. Kenan-Eichler M, Leshkowitz D, Tal L, Noor E, Melamed-Bessudo C, et al: Wheat hybridization and polyploidization results in deregulation of small RNAs. Genetics 188:263-272 (2011).
  104. Kidwell MG, Kidwell JF, Sved JA: Hybrid dysgenesis in Drosophila melanogaster: A syndrome of aberrant traits including mutation, sterility and male recombination. Genetics 86:813-833 (1977).

    External Resources

  105. Kirino Y, Kim N, de Planell-Saguer M, Khandros E, Chiorean S, et al: Arginine methylation of Piwi proteins catalysed by dPRMT5 is required for Ago3 and Aub stability. Nat Cell Biol 11:652-658 (2009).
  106. Labrador M, Farre M, Utzet F, Fontdevila A: Interspecific hybridization increases transposition rates of Osvaldo. Mol Biol Evol 16:931-937 (1999).

    External Resources

  107. Lamatsch DK, Stöck M: Sperm-dependent parthenogenesis and hybridogenesis in teleost fishes, in Schön I, Martens K, van Dijk P (eds): Lost Sex, pp 399-432 (Springer, Berlin 2009).

    External Resources

  108. Lau NC: Analysis of small endogenous RNAs. Curr Protoc Mol Biol, Chapter 26:Unit26.7 (2008).
  109. Lau NC, Ohsumi T, Borowsky M, Kingston RE, Blower MD: Systematic and single cell analysis of Xenopus Piwi-interacting RNAs and Xiwi. EMBO J 28:2945-2958 (2009).
  110. Lee HC, Gu W, Shirayama M, Youngman E, Conte D Jr, Mello CC: C. elegans piRNAs mediate the genome-wide surveillance of germline transcripts. Cell 150:78-87 (2012).
  111. Levin HL, Moran JV: Dynamic interactions between transposable elements and their hosts. Nat Rev Genet 12:615-627 (2011).
  112. Li C, Vagin VV, Lee S, Xu J, Ma S, et al: Collapse of germline piRNAs in the absence of Argonaute3 reveals somatic piRNAs in flies. Cell 137:509-521 (2009).
  113. Liu D, You C, Liu S, Liu L, Duan W, et al: Characterization of a novel Tc1-like transposon from bream (Cyprinidae, Megalobrama) and its genetic variation in the polyploidy progeny of bream-red crucian carp crosses. J Mol Evol 69:395-403 (2009).
  114. Lozovskaya ER, Scheinker VS, Evgen'ev MB: A hybrid dysgenesis syndrome in Drosophila virilis. Genetics 126:619-623 (1990).

    External Resources

  115. Lutes AA, Baumann DP, Neaves WB, Baumann P: Laboratory synthesis of an independently reproducing vertebrate species. Proc Natl Acad Sci USA 108:9910-9915 (2011).
  116. Lynch M, Conery JS: The evolutionary fate and consequences of duplicate genes. Science 290:1151-1155 (2000).
  117. Mable BK: Sex in the postgenomic era. Trends Ecol Evol 22:559-561 (2007).
  118. Malone JH, Michalak P: Gene expression analysis of the ovary of hybrid females of Xenopus laevis and X. muelleri. BMC Evol Biol 8:82 (2008a).
  119. Malone JH, Michalak P: Physiological sex predicts hybrid sterility regardless of genotype. Science 319:59 (2008b).
  120. Malone JH, Chrzanowski TH, Michalak P: Sterility and gene expression in hybrid males of Xenopus laevis and X. muelleri. PLoS One 2:e781 (2007).
  121. Mark Welch D, Meselson M: Evidence for the evolution of bdelloid rotifers without sexual reproduction or genetic exchange. Science 288:1211-1215 (2000).
  122. Mark Welch DB, Mark Welch JL, Meselson M: Evidence for degenerate tetraploidy in bdelloid rotifers. Proc Natl Acad Sci USA 105:5145-5149 (2008).
  123. Mark Welch DB, Ricci C, Meselson M: Bdelloid rotifers: progress in understanding the success of an evolutionary scandal, in Schön I, Martens K, van Dijk P (eds): Lost Sex, pp 259-279 (Springer, Berlin 2009).

    External Resources

  124. Marracci S, Batistoni R, Pesole G, Citti L, Nardi I: Gypsy/Ty3-like elements in the genome of the terrestrial salamander Hydromantes (Amphibia, Urodela). J Mol Evol 43:584-593 (1996).
  125. Martienssen RA: Heterochromatin, small RNA and post-fertilization dysgenesis in allopolyploid and interploid hybrids of Arabidopsis. New Phytol 186:46-53 (2010).
  126. Matveev V, Okada N: Retroposons of salmonoid fishes (Actinopterygii: Salmonoidei) and their evolution. Gene 434:16-28 (2009).
  127. Matzke MA, Matzke AJM: Polyploidy and transposons. Trends Ecol Evol 13:241 (1998).
  128. Matzke MA, Scheid OM, Matzke AJM: Rapid structural and epigenetic changes in polyploid and aneuploid genomes. Bioessays 21:761-767 (1999).
  129. McClintock B: The significance of responses of the genome to challenge. Science 226:792-801 (1984).
  130. Mergeay J, Aguilera X, Declerck S, Petrusek A, Huyse T, De Meester L: The genetic legacy of polyploid Bolivian Daphnia: the tropical Andes as a source for the North and South American D. pulicaria complex. Mol Ecol 17:1789-800 (2008).
  131. Michalak P: Epigenetic, transposon and small RNA determinants of hybrid dysfunctions. Heredity 102:45-50 (2009).
  132. Michalak P: An eruption of mobile elements in genomes of hybrid sunflowers. Heredity 104:329-330 (2010).
  133. Michalak P, Malone JH: Testis-derived microRNA profiles of African clawed frogs (Xenopus) and their sterile hybrids. Genomics 91:158-164 (2008).
  134. Miller HC, Biggs PJ, Voelckel C, Nelson NJ: De novo sequence assembly and characterisation of a partial transcriptome for an evolutionarily distinct reptile, the tuatara (Sphenodon punctatus). BMC Genomics 13:439 (2012).
  135. Mizuno K, Miyabe I, Schalbetter SA, Carr AM, Murray JM: Recombination-restarted replication makes inverted chromosome fusions at inverted repeats. Nature 493:246-249 (2013).
  136. Mochizuki K, Fine NA, Fujisawa T, Gorovsky MA: Analysis of a piwi-related gene implicates small RNAs in genome rearrangement in Tetrahymena. Cell 110:689-699 (2002).
  137. Mouse Genome Sequencing Consortium: Initial sequencing and comparative analysis of the mouse genome. Nature 420:520-562 (2002).
  138. Murchison EP, Kheradpour P, Sachidanandam R, Smith C, Hodges E, et al: Conservation of small RNA pathways in platypus. Genome Res 18:995-1004 (2008).
  139. Neaves WB, Baumann P: Unisexual reproduction among vertebrates. Trends Genet 27:81-88 (2011).
  140. Nene V, Wortman JR, Lawson D, Haas B, Kodira C, et al: Genome sequence of Aedes aegypti, a major arbovirus vector. Science 316:1718-1723 (2007).
  141. Normark BB: The evolution of alternative genetic systems in insects. Annu Rev Entomol 48:397-423 (2003).
  142. Novick P, Smith J, Ray D, Boissinot S: Independent and parallel lateral transfer of DNA transposons in tetrapod genomes. Gene 449:85-94 (2010).
  143. Novick PA, Smith JD, Floumanhaft M, Ray DA, Boissinot S: The evolution and diversity of DNA transposons in the genome of the lizard Anolis carolinensis. Genome Biol Evol 3:1-14 (2011).
  144. Obbard DJ, Gordon KH, Buck AH, Jiggins FM: The evolution of RNAi as a defence against viruses and transposable elements. Philos Trans R Soc Lond B Biol Sci 364:99-115 (2009).
  145. O'Meally D, Miller H, Patel HR, Graves JA, Ezaz T: The first cytogenetic map of the tuatara, Sphenodon punctatus. Cytogenet Genome Res 127:213-223 (2009).
  146. O'Neill RJ, O'Neill MJ, Graves JA: Undermethylation associated with retroelement activation and chromosome remodelling in an interspecific mammalian hybrid. Nature 393:68-72 (1998).
  147. O'Neill RJ, Eldridge MD, Graves JA: Chromosome heterozygosity and de novo chromosome rearrangements in mammalian interspecies hybrids. Mamm Genome 12:256-259 (2001).
  148. Orsi GA, Joyce EF, Couble P, McKim KS, Loppin B: Drosophila I-R hybrid dysgenesis is associated with catastrophic meiosis and abnormal zygote formation. J Cell Sci 123:3515-3524 (2010).
  149. Otto SP, Whitton J: Polyploid incidence and evolution. Annu Rev Genet 34:401-437 (2000).
  150. Parisod C, Alix K, Just J, Petit M, Sarilar V, et al: Impact of transposable elements on the organization and function of allopolyploid genomes. New Phytol 186:37-45 (2010).
  151. Pelisson A, Song SU, Prud'homme N, Smith PA, Bucheton A, Corces VG: Gypsy transposition correlates with the production of a retroviral envelope-like protein under the tissue-specific control of the Drosophila flamenco gene. EMBO J 13:4401-4411 (1994).

    External Resources

  152. Petrov DA, Schutzman JL, Hartl DL, Lozovskaya ER: Diverse transposable elements are mobilized in hybrid dysgenesis in Drosophila virilis. Proc Natl Acad Sci USA 92:8050-8054 (1995).
  153. Picard G, L'Héritier P: A maternally inherited factor inducing sterility in Drosophila melanogaster. Drosophila Inf Serv 46:54 (1971).
  154. Prescott DM: Genome gymnastics: unique modes of DNA evolution and processing in ciliates. Nat Rev Genet 1:191-198 (2000).
  155. Pritham EJ, Putliwala T, Feschotte C: Mavericks, a novel class of giant transposable elements widespread in eukaryotes and related to DNA viruses. Gene 390:3-17 (2007).
  156. Renfree MB, Papenfuss AT, Deakin JE, Lindsay J, Heider T, et al: Genome sequence of an Australian kangaroo, Macropus eugenii, provides insight into the evolution of mammalian reproduction and development. Genome Biol 12:R81 (2011).
  157. Rho M, Schaack S, Gao X, Kim S, Lynch M, Tang H: LTR retroelements in the genome of Daphnia pulex. BMC Genomics 11:425 (2010).
  158. Rizzon C, Marais G, Gouy M, Biémont C: Recombination rate and the distribution of transposable elements in the Drosophila melanogaster genome. Genome Res 12:400-407 (2002).
  159. Rozhkov NV, Aravin AA, Zelentsova ES, Schostak NG, Sachidanandam R, et al: Small RNA-based silencing strategies for transposons in the process of invading Drosophila species. RNA 16:1634-1645 (2010).
  160. Rozhkov NV, Schostak NG, Zelentsova ES, Yushenova IA, Zatsepina OG, Evgen'ev MB: Evolution and dynamics of small RNA response to a retroelement invasion in Drosophila. Mol Biol Evol 30:397-408 (2013).
  161. Saleh MC, Tassetto M, van Rij RP, Goic B, Gausson V, et al: Antiviral immunity in Drosophila requires systematic RNA interference spread. Nature 458:346-350 (2009).
  162. Schaack S, Pritham EJ, Wolf A, Lynch M: DNA transposon dynamics in populations of Daphnia pulex with and without sex. Proc Biol Sci 277:2381-2387 (2010a).
  163. Schaack S, Choi E, Lynch M, Pritham EJ: DNA transposons and the role of recombination in mutation accumulation in Daphnia pulex. Genome Biol 11:R46 (2010b).
  164. Schnable PS, Ware D, Fulton RS, Stein JC, Wei F, et al: The B73 maize genome: complexity, diversity, and dynamics. Science 326:1112-1115 (2009).
  165. Schön I, Martens K, van Dijk P (eds): Lost Sex: The Evolutionary Biology of Parthenogenesis (Springer, Berlin 2009).

    External Resources

  166. Schütt S, Florl AR, Shi W, Hemberger M, Orth A, et al: DNA methylation in placentas of interspecies mouse hybrids. Genetics 165:223-228 (2003).

    External Resources

  167. Semon M, Wolfe KH: Consequences of genome duplication. Curr Opin Genet Dev 17:505-512 (2007).
  168. Shedlock AM: Phylogenomic investigation of CR1 LINE diversity in reptiles. Syst Biol 55:902-911 (2006).
  169. Shedlock AM, Botka CW, Zhao S, Shetty J, Zhang T, et al: Phylogenomics of nonavian reptiles and the structure of the ancestral amniote genome. Proc Natl Acad Sci USA 104:2767-2772 (2007).
  170. Shirayama M, Seth M, Lee HC, Gu W, Ishidate T, et al: piRNAs initiate an epigenetic memory of nonself RNA in the C. elegans germline. Cell 150:65-77 (2012).
  171. Siomi MC, Saito K, Siomi H: How selfish retrotransposons are silenced in Drosophila germline and somatic cells. FEBS Lett 582:2473-2478 (2008).
  172. Siomi MC, Sato K, Pezic D, Aravin A: PIWI-interacting small RNAs: the vanguard of genome defence. Nat Rev Mol Cell Biol 12:246-258 (2011).
  173. Soltis PS, Soltis DE: Polyploidy and genome evolution (Springer, Berlin 2012).

    External Resources

  174. Song K, Lu P, Tang K, Osborn TC: Rapid genome change in synthetic polyploids of Brassica and its implications for polyploid evolution. Proc Natl Acad Sci USA 92:7719-7723 (1995).
  175. Sontheimer EJ: Small RNAs of opposite sign… but same absolute value. Cell 151:1157-1158 (2012).
  176. Suárez-Villota EY, Vargas RA, Marchant CL, Torres JE, Köhler N, et al: Distribution of repetitive DNAs and the hybrid origin of the red vizcacha rat (Octodontidae). Genome 55:105-117 (2012).
  177. Sun C, Shepard DB, Chong RA, López Arriaza J, Hall K, et al: LTR retrotransposons contribute to genomic gigantism in plethodontid salamanders. Genome Biol Evol 4:168-183 (2012a).
  178. Sun C, López Arriaza JR, Mueller RL: Slow DNA loss in the gigantic genomes of salamanders. Genome Biol Evol 4:1340-1348 (2012b).
  179. Svartman M, Stone G, Stanyon R: Molecular cytogenetics discards polyploidy in mammals. Genomics 85:425-430 (2005).
  180. Thomas CA: The genetic organization of chromosomes. Annu Rev Genet 5:237-256 (1971).
  181. Tollis M, Boissinot S: The transposable element profile of the anolis genome. Mob Genet Elements 1:107-111 (2011).
  182. Torti C, Malacrida A, Yannopoulos G, Louis C, Gasperi G: Hybrid dysgenesis-like phenomena in the medfly, Ceratitis capitata (Diptera, Tephritidae). J Hered 85:92-99 (1994).
  183. Vagin VV, Klenov MS, Kalmykova AI, Stolyarenko AD, Kotelnikov RN, Gvozdev VA: The RNA interference proteins and vasa locus are involved in the silencing of retrotransposons in the female germline of Drosophila melanogaster. RNA Biol 1:54-58 (2004).
  184. Vagin VV, Sigova A, Li C, Seitz H, Gvozdev V, Zamore PD: A distinct small RNA pathway silences selfish genetic elements in the germline. Science 313:320-324 (2006).
  185. Valizadeh P, Crease TJ: The association between breeding system and transposable element dynamics in Daphnia pulex. J Mol Evol 66:643-654 (2008).
  186. Vergilino R, Belzile C, Dufresne F: Genome size evolution and polyploidy in the Daphnia pulex complex (Cladocera: Daphniidae). Biol J Linn Soc 97:68-79 (2009).

    External Resources

  187. Vergilino R, Elliott TA, Desjardins-Proulx P, Crease TJ, Dufresne F: Evolution of a transposon in Daphnia hybrid genomes. Mob DNA 4:7 (2013).
  188. Vermaak D, Henikoff S, Malik HS: Positive selection drives the evolution of rhino, a member of the heterochromatin protein 1 family in Drosophila. PLoS Genet 1:96-108 (2005).
  189. Vieira J, Vieira CP, Hartl DL, Lozovskaya ER: Factors contributing to the hybrid dysgenesis syndrome in Drosophila virilis. Genet Res 71:109-117 (1998).
  190. Vitte C, Panaud O: LTR retrotransposons and flowering plant genome size: emergence of the increase/decrease model. Cytogenet Genome Res 110:91-107 (2005).
  191. Voss SR, Kump DK, Putta S, Pauly N, Reynolds A, et al: Origin of amphibian and avian chromosomes by fission, fusion, and retention of ancestral chromosomes. Genome Res 21:1306-1312 (2011).
  192. Wang Z, Miyake T, Edwards SV, Amemiya CT: Tuatara (Sphenodon) genomics: BAC library construction, sequence survey, and application to the DMRT gene family. J Hered 97:541-548 (2006).
  193. Wolfe KH: Yesterday's polyploids and the mystery of diploidization. Nat Rev Genet 2:333-341 (2001).
  194. Yoder JA, Walsh CP, Bestor TH: Cytosine methylation and the ecology of intragenomic parasites. Trends Genet 13:335-340 (1997).
  195. Zelentsova H, Poluectova H, Mnjoian L, Lyozin G, Veleikodvorskaja V, et al: Distribution and evolution of mobile elements in the virilis species group of Drosophila. Chromosoma 108:443-456 (1999).