The Tvv1 retrotransposon family is conserved between plant genomes separated by over 100 million years

Theoretical and Applied Genetics

Volumn 127, Issue 5, 2014, Pages 1223-1235

  Moisy, Cédric ^a,b,c   Schulman, Alan H ^a,b   Kalendar, Ruslan ^a   Buchmann, Jan P ^a   Pelsy, Frédérique ^d,e  

^a UNIVERSITY OF HELSINKI   (Finland)

^b FINNISH FOREST RESEARCH INSTITUTE   (Finland)

^c UMR AGAP   (France)

^d UNIVERSITÉ DE STRASBOURG   (France)

^e UNIVERSITÉ DE STRASBOURG   (France)

Author keywords

[No Author keywords available]

Indexed keywords

FORESTRY;

COMPARATIVE ANALYSIS; CULTIVATED POTATO; DICOTYLEDONOUS PLANTS; METAPOPULATIONS; MOLECULAR MARKER; RETROTRANSPOSON; VASCULAR PLANT; VITIS VINIFERA;

GENES;

ASTERIDS; LYCOPERSICON ESCULENTUM; ROSIDS; SOLANUM DEMISSUM; SOLANUM JAMESII; SOLANUM TUBEROSUM; TRACHEOPHYTA; VITIS; VITIS VINIFERA;

RETROPOSON;

BARREL MEDIC; DNA SEQUENCE; GENE DOSAGE; GENETICS; MAIZE; NUCLEOTIDE SEQUENCE; PHYLOGENY; PLANT GENOME; RETROPOSON; RICE; SOLANUM; VITIS;

CONSERVED SEQUENCE; GENE DOSAGE; GENOME, PLANT; MEDICAGO TRUNCATULA; ORYZA SATIVA; PHYLOGENY; RETROELEMENTS; SEQUENCE ANALYSIS, DNA; SOLANUM; VITIS; ZEA MAYS;

EID: 84907201040     PISSN: 00405752     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00122-014-2293-z     Document Type: Article

References (66)

1. Abram M, Ferris A, Shao W, Alvord W, Hughes S (2010) Nature, position, and frequency of mutations made in a single cycle of HIV-1 replication. J Virol 84: 9864-9878.
2. Baucom RS, Estill JC, Leebens-Mack J, Bennetzen JL (2009) Natural selection on gene function drives the evolution of LTR retrotransposon families in the rice genome. Genome Res 19: 243-254.
3. Boutabout M, Wilhelm M, Wilhelm FX (2001) DNA synthesis fidelity by the reverse transcriptase of the yeast retrotransposon Ty1. Nucleic Acids Res 29: 2217-2222.
4. Bowen NJ, Mcdonald JF (1999) Genomic analysis of Caenorhabditis elegans reveals ancient families of retroviral-like elements. Genome Res 9: 924-935.
5. Casacuberta JM, Vernhettes S, Grandbastien MA (1995) Sequence variability within the tobacco retrotransposon Tnt1 population. EMBO J 14: 2670-2678.
6. Cenci A, Combes M-C, Lashermes P (2010) Comparative sequence analyses indicate that Coffea (Asterids) and Vitis (Rosids) derive from the same paleo-hexaploid ancestral genome. Mol Gen Genet 283: 493-501.
7. The Angiosperm Phylogeny Group (2009) An update of the Angiosperm Phylogeny Group classification for the orders and families of flowering plants: APG III. Bot J Linn Soc 161: 105-121.
8. Cheng X, Zhang D, Cheng Z, Keller B, Ling H-Q (2009) A new family of Ty1-copia-Like retrotransposons originated in the tomato genome by a recent horizontal transfer event. Genetics 181: 1183-1193.
9. Dixit A, Ma K-H, Yu J-W, Cho E-G, Park Y-J (2006) Reverse transcriptase domain sequences from Mungbean (Vigna radiata) LTR retrotransposons: sequence characterization and phylogenetic analysis. Plant Cell Rep 25: 100-111.
10. Domingo E (2002) Quasispecies theory in virology. J Virol 76: 463-465.
11. Edgar RC (2004) MUSCLE: a multiple sequence alignment method with reduced time and space complexity. BMC Bioinforma 5: 113. doi: 10. 1186/1471-2105-5-113.
12. Eickbush TH, Jamburuthugoda VK (2008) The diversity of retrotransposons and the properties of their reverse transcriptases. Virus Res 134: 221-234.
13. Fortune PM, Roulin A, Panaud O (2008) Horizontal transfer of transposable elements in plants. Commun Integr Biol 1: 74-77.
14. Gabriel A, Willems M, Mules EH, Boeke JD (1996) Replication infidelity during a single cycle of Ty1 retrotransposition. Proc Natl Acad Sci USA 93: 7767-7771.
15. Gómez E, Schulman AH, Martínez-Izquierdo JA, Vicient CM (2006) Integrase diversity and transcription of the maize retrotransposon Grande. Genome 49: 558-562.
16. Hanski I (1998) Metapopulation dynamics. Nature 396: 41-49.
17. Jansen RK, Kaittanis C, Saski C, Lee S-B, Tomkins J, Alverson AJ, Daniell H (2006) Phylogenetic analyses of Vitis (Vitaceae) based on complete chloroplast genome sequences: effects of taxon sampling and phylogenetic methods on resolving relationships among rosids. BMC Evol Biol 6: 32.
18. Kalendar R, Tanskanen J, Immonen S, Nevo E, Schulman AH (2000) Genome evolution of wild barley (Hordeum spontaneum) by BARE-1 retrotransposon dynamics in response to sharp microclimatic divergence. Proc Natl Acad Sci USA 97: 6603-6607.
19. Kalendar R, Tanskanen J, Chang W, Antonius K, Sela H, Peleg O, Schulman AH (2008) Cassandra retrotransposons carry independently transcribed 5S RNA. Proc Natl Acad Sci USA 105: 5833-5838.
20. Kalendar R, Lee D, Schulman AH (2011) Java web tools for PCR, in silico PCR, and oligonucleotide assembly and analysis. Genomics 98: 137-144.
21. Kapitonov VV, Jurka J (2008) A universal classification of eukaryotic transposable elements implemented in Repbase. Nat Rev Genet 9: 411-412.
22. Kidwell MG, Lisch DR (2001) Perspective: transposable elements, parasitic DNA, and genome evolution. Evolution 55: 1-24.
23. Koch MA, Haubold B, Mitchell-Olds T (2000) Comparative evolutionary analysis of chalcone synthase and alcohol dehydrogenase loci in Arabidopsis, Arabis, and related genera (Brassicaceae). Mol Biol Evol 17: 1483-1498.
24. Kumar A, Bennetzen JL (1999) Plant retrotransposons. Annu Rev Genet 33: 479-532.
25. Le Rouzic A, Boutin TS, Capy P (2007) Long-term evolution of transposable elements. Proc Natl Acad Sci USA 104: 19375-19380.
26. Llorens C, Muñoz-Pomer A, Bernad L, Botella H, Moya A (2009) Network dynamics of eukaryotic LTR retroelements beyond phylogenetic trees. Biol Direct 4: 41.
27. Lohe AR, Moriyama EN, Lidholm DA, Hartl DL (1995) Horizontal transmission, vertical inactivation, and stochastic loss of marinerlike transposable elements. Mol Biol Evol 12: 62-72.
28. Macas J, Koblízková A, Navrátilová A, Neumann P (2009) Hypervariable 3′ UTR region of plant LTR-retrotransposons as a source of novel satellite repeats. Gene 448: 198-206.
29. Manetti ME, Rossi M, Nakabashi M, Grandbastien MA, Van Sluys MA (2009) The Tnt1 family member Retrosol copy number and structure disclose retrotransposon diversification in different Solanum species. Mol Gen Genet 281: 261-271.
30. Moisy C, Blanc S, Merdinoglu D, Pelsy F (2008a) Structural variability of Tvv1 grapevine retrotransposons can be caused by illegitimate recombination. Theor Appl Genet 116: 671-682.
31. Moisy C, Garrison KE, Meredith CP, Pelsy F (2008b) Characterization of ten novel Ty1/copia-like retrotransposon families of the grapevine. BMC Genomics 9: 1-14.
32. Nielen S, Campos-Fonseca F, Leal-Bertioli S, Guimarães P, Seijo G, Town C, Arrial R et al (2010) FIDEL-a retrovirus-like retrotransposon and its distinct evolutionary histories in the A-and B-genome components of cultivated peanut. Chromosome Res 18(2): 227-246.
33. Ojosnegros S, Perales C, Mas A, Domingo E (2011) Quasispecies as a matter of fact: viruses and beyond. Virus Res 162(1-2): 203-215.
34. Otto TD, Gomes LH, Alves-Ferreira M, De Miranda AB, Degrave WM (2008) ReRep: computational detection of repetitive sequences in genome survey sequences (GSS). BMC Bioinforma 9: 366.
35. Pelsy F (2007) Untranslated leader region polymorphism of Tvv1, a retrotransposon family, is a novel marker useful for analyzing genetic diversity and relatedness in the genus Vitis. Theor Appl Genet 116: 15-27.
36. Pelsy F, Merdinoglu D (2002) Complete sequence of Tvv1, a family of Ty 1 copia-like retrotransposons of Vitis vinifera L., reconstituted by chromosome walking. Theor Appl Genet 105: 614-621.
37. Preston BD (1996) Error-prone retrotransposition: rime of the ancient mutators. Proc Natl Acad Sci USA 93: 7427-7431.
38. Rice P, Longden I, Bleasby A (2000) EMBOSS: the European molecular biology open software suite. Trends Genet 16: 276-277.
39. Roulin A, Piegu B, Wing R, Panaud O (2008) Evidence of multiple horizontal transfers of the long terminal repeat retrotransposon RIRE1 within the genus Oryza. Plant J 53: 950-959.
40. Roulin A, Piegu B, Fortune PM, Sabot F, D'Hont A, Manicacci D, Panaud O (2009) Whole genome surveys of rice, maize and sorghum reveal multiple horizontal transfers of the LTR-retrotransposon Route66 in Poaceae. BMC Evol Biol 9: 58.
41. Rozen S, Skaletsky H (2000) Primer3 on the WWW for general users and for biologist programmers. Methods Mol Biol 132: 365-386.
42. Sabot F, Schulman AH (2006) Parasitism and the retrotransposon life cycle in plants: a hitchhiker's guide to the genome. Heredity 97: 381-388.
43. Sabot F, Schulman AH (2007) Template switching can create complex LTR retrotransposon insertions in Triticeae genomes. BMC Genomics 8: 247.
44. SanMiguel P, Gaut BS, Tikhonov A, Nakajima Y, Bennetzen JL (1998) The paleontology of intergene retrotransposons of maize. Nat Genet 20: 43-45.
45. Schnable PS, Ware D, Fulton RS, Stein JC, Wei F, Pasternak S, Liang C, Zhang J, Fulton L, Graves TA et al (2009) The B73 maize genome: complexity, diversity, and dynamics. Science 326: 1112-1115.
46. Schulman AH (2013) Retrotransposon replication in plants. Curr Opin Virol 3(6): 604-614.
47. Schulman AH, Wicker T (2013) A field guide to transposable elements. In: Fedoroff NV (ed) Plant transposons and genome dynamics in evolution. Wiley, Hoboken, pp 15-40.
48. Shirasu K, Schulman AH, Lahaye T, Schulze-Lefert P (2000) A contiguous 66-kb barley DNA sequence provides evidence for reversible genome expansion. Genome Res 10: 908-915.
49. Smith RA, Anderson DJ, Preston BD (2004) Purifying selection masks the mutational flexibility of HIV-1 reverse transcriptase. J Biol Chem 279: 26726-26734.
50. Stuart-Rogers C, Flavell AJ (2001) The evolution of Ty1-copia group retrotransposons in gymnosperms. Mol Biol Evol 18: 155-163.
51. Suoniemi A, Tanskanen J, Pentikäinen O, Johnson MS, Schulman AH (1998) The core domain of retrotransposon integrase in Hordeum: predicted structure and evolution. Mol Biol Evol 15: 1135-1144.
52. Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S (2011) MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 28(10): 2731-2739.
53. Tanskanen J, Sabot F, Vicient CM, Schulman AH (2007) Life without GAG: the BARE-2 retrotransposon as a parasite's parasite. Gene 390: 166-174.
54. Vershinin AV, Ellis TH (1999) Heterogeneity of the internal structure of PDR1, a family of Ty1/copia-like retrotransposons in pea. Mol Gen Genet 262: 703-713.
55. Vicient CM, Kalendar R, Schulman AH (2005) Variability, recombination, and mosaic evolution of the barley BARE-1 retrotransposon. J Mol Evol 61: 275-291.
56. Vitte C, Chaparro C, Quesneville H, Panaud O (2007a) Spip and Squiq, two novel rice non-autonomous LTR retro-element families related to RIRE3 and RIRE8. Plant Sci 172: 8-19.
57. Vitte C, Panaud O, Quesneville H (2007b) LTR retrotransposons in rice (Oryza sativa, L.): recent burst amplifications followed by rapid DNA loss. BMC Genomics 8: 218.
58. Wang H, Moore MJ, Soltis PS, Bell CD, Brockington SF, Alexandre R, Davis CC, Latvis M, Manchester SR, Soltis DE (2009) Rosid radiation and the rapid rise of angiosperm-dominated forests. Proc Natl Acad Sci USA 106: 3853-3858.
59. Wawrzynski A, Ashfield T, Chen NWG, Mammadov J, Nguyen A, Podicheti R, Cannon SB, Thareau V, Ameline-Torregrosa C, Cannon E et al (2008) Replication of nonautonomous retroelements in soybean appears to be both recent and common. Plant Physiol 148: 1760-1771.
60. Wicker T, Keller B (2007) Genome-wide comparative analysis of copia retrotransposons in Triticeae, rice, and Arabidopsis reveals conserved ancient evolutionary lineages and distinct dynamics of individual copia families. Genome Res 17(7): 1072-1081.
61. Wicker T, Schlagenhauf E, Graner A, Close TJ, Keller B, Stein N (2006) 454 sequencing put to the test using the complex genome of barley. BMC Genomics 7: 275.
62. Wicker T, Sabot F, Hua-Van A, Bennetzen JL, Capy P, Chalhoub B, Flavell AJ, Leroy P, Morgante M, Panaud O et al (2007) A unified classification system for eukaryotic transposable elements. Nat Rev Genet 8: 973-982.
63. Wicker T, Taudien S, Houben A, Keller B, Graner A, Platzer M, Stein N (2009) A whole-genome snapshot of 454 sequences exposes the composition of the barley genome and provides evidence for parallel evolution of genome size in wheat and barley. Plant J 59: 712-722.
64. Wilhelm M, Wilhelm FX (2001) Reverse transcription of retroviruses and LTR retrotransposons. Cell Mol Life Sci 58: 1246-1262.
65. Witte CP, Le QH, Bureau T, Kumar A (2001) Terminal-repeat retrotransposons in miniature (TRIM) are involved in restructuring plant genomes. Proc Natl Acad Sci USA 98: 13778.
66. Zhang Z, Schwartz S, Wagner L, Miller W (2000) A greedy algorithm for aligning DNA sequences. J Comput Biol 7: 203-214.