The Ty1-copia families SALIRE and Cotzilla populating the Beta vulgaris genome show remarkable differences in abundance, chromosomal distribution, and age

Chromosome Research

Volumn 18, Issue 2, 2010, Pages 247-263

  Weber, Beatrice ^a   Wenke, Torsten ^a   Frömmel, Ulrike ^a   Schmidt, Thomas ^a   Heitkam, Tony ^a  

^a DRESDEN UNIVERSITY OF TECHNOLOGY   (Germany)

Author keywords

Fish; LTR retrotransposon; Sirevirus; Sugar beet; Ty1 copie

Indexed keywords

GENOMIC DNA; PLANT DNA;

ARTICLE; BEET; BINDING SITE; CELL LINEAGE; COTZILLA; DNA DETERMINATION; DNA METHYLATION; EUCHROMATIN; EUKARYOTE; FLUORESCENCE IN SITU HYBRIDIZATION; GENE INSERTION; GENETIC HETEROGENEITY; GENETIC VARIABILITY; GENOME SIZE; HETEROCHROMATIN; LONG TERMINAL REPEAT; MOLECULAR EVOLUTION; NONHUMAN; NUCLEOTIDE SEQUENCE; OPEN READING FRAME; PLANT GENETICS; PLANT GENOME; PRIORITY JOURNAL; PROTEIN BINDING; RETROPOSON; SALIRE; SEQUENCE ALIGNMENT; TY1 COPIA;

BETA VULGARIS; CHROMOSOMES, PLANT; PHYLOGENY; RETROELEMENTS; TERMINAL REPEAT SEQUENCES;

BETA VULGARIS; BETA VULGARIS SUBSP. VULGARIS;

EID: 77950460688     PISSN: 09673849     EISSN: 15736849     Source Type: Journal    
DOI: 10.1007/s10577-009-9104-4     Document Type: Article

References (78)

1. Ammuganathan K, Earle E (1991) Nuclear DNA content of some important plant species. Plant Mol Biol Report 9: 208-218
2. Bennetzen JL (2002) Mechanisms and rates of genome expansion and contraction in flowering plants. Genetica 115: 29-36
3. Birney E, Clamp M, Durbin R (2004) Gene Wise and Genomewise. Genome Res 14: 988-995
4. Boeke JD, Corces VG (1989) Transcription and reverse transcription of retrotransposons. Annu Rev Microbiol 43: 403-434
5. Brandes A, Heslop-Harrison JS, Kamm A, Kubis S, Doudrick RL, Schmidt T (1997) Comparative analysis of the chromosomal and genomic organization of Ty1-copio-like retrotransposons in pteridophytes, gymnosperms and angiosperms. Plant Mol Biol 33: 11-21 (Pubitemid 27111794)
6. Casacuberta JM, Vernhettes S, Audeon C, Grandbastien MA (1997) Quasispecies in retrotransposons: A role for sequence variability in Tnt1 evolution. Genetica 100:109-117 (Pubitemid 28034757)
7. Dechyeva D, Gindullis F, Schmidt T (2003) Divergence of satellite DNA and interspersion of dispersed repeats in the genome of the wild beet Beta procumbens. Chromosome Res 11: 3-21 (Pubitemid 36315354)
8. de Felice B, Wilson R, Argenziano C, Kafantaris I, Conicella C (2008) A transcriptionally active copia-like retroelement in Citrus limon. Cell Mol Biol Lett. doi: 10.2478/s11658-008-0050-5
9. de Jong HJ, Fransz P, Zabel P (1999) High resolution FISH in plants-techniques and applications. Trends Plant Sci 4: 258-263 (Pubitemid 29319501)
10. Desel C, Jung C, Cai D, Kleine M, Schmidt T (2001) Highresolution mapping of YACs and the single-copy gene Hslprol on Beta vulgaris chromosomes by multi-colour fluorescence in situ hybridization. Plant Mol Biol 45: 113-122
11. Devos KM, Brown JKM, Bennetzen JL (2002) Genome size reduction through illegitimate recombination counteracts genome expansion in Arabidopsis. Genome Res 12: 1075-1079
12. Edgar R (2004) MUSCLE: a multiple sequence alignment method with reduced time and space complexity. BMC Bioinformatics 5: 113
13. Francki MG (2001) Identification of Bilby, a diverged centromeric Ty1 -copia retrotransposon family from cereal rye (Secale cereale L.). Genome 44: 266-274
14. Gallo SA, Finnegan CM, Viard M et al (2003) The HIV Env-mediated fusion reaction. BBA - Biomembranes 1614: 36-50
15. Gao X, Havecker ER, Baranov PV, Atkins JF, Voytas DF (2003) Translational recoding signals between gag and pol in diverse LTR retrotransposons. RNA 9: 1422-1430
16. Gindullis F, Dechyeva D, Schmidt T (2001a) Construction and characterization of a BAC library for the molecular dissection of a single wild beet centromere and sugar beet (Beta vulgaris) genome analysis. Genome 44: 846-855
17. Gindullis F, Desel C, Galasso I, Schmidt T (2001b) The largescale organization of the centromeric region in Beta species. Genome Res 11: 253-265
18. Grandbastien MA, Audeon C, Casacuberta JM et al (1994) Functional analysis of the tobacco Tnt1 retrotransposon. Genetica 93: 181-189
19. Havecker ER, Gao X, Voytas DF (2005) The Sireviruses, a plant-specific lineage of the copia retrotransposons, interact with a family of proteins related to dynein light chain 8. Plant Physiol 139: 857-868
20. Heslop-Harrison JS, Schwarzacher T, Anamthawat-Jonsson K, Leitch AR, Shi M, Leitch IJ (1991) In-situ hybridization with automated chromosome denaturation. Technique 3: 109-116
21. Heslop-Harrison JS, Brandes A, Taketa S et al (1997) The chromosomal distributions of Ty1 -copia group retrotransposable elements in higher plants and their implications for genome evolution. Genetica 100: 197-204
22. Higo K, Ugawa Y, Iwamoto M, Korenaga T (1999) Plant cisacting regulatory DNA elements (PLACE) database. Nucleic Acids Res 27: 297-300 (Pubitemid 29209466)
23. Hirochika H, Fukuchi A, Kikuchi F (1992) Retrotransposon families in rice. Mol Gen Genet 233: 209-216
24. Hirochika H, Otsuki H, Yoshikawa M, Otsuki Y, Sugimoto K, Takeda S (1996) Autonomous transposition of the tobacco retrotransposon Tto1in rice.Plant Cell 8:725-734 (Pubitemid 126632553)
25. Holligan D, Zhang X, Jiang N, Pritham EJ, Wessler SR (2006) The transposable element landscape of the model legume Lotus japonicas. Genetics 174: 2215-2228
26. Hull R (2001) Classifying reverse transcribing elements: a proposal and a challenge to the ICTV Arch Virol 146: 2255-2261
27. Jia J, Yang Z, Li G, Liu C, Lei M, Zhang T, Zhou J, Ren Z (2009) Isolation and chromosomal distribution of a novel Tyl-copia-like sequence from Secale, which enables identification of wheat-Secale africanum introgression lines. J Appl Genet 50: 25-28
28. Kapitonov V, Jurka J (1999) Molecular paleontology of transposable elements from Arabidopsis thaliana. Genetica 107: 27-37
29. Kimura Y, Tosa Y, Shimada S, Sogo R, Kusaba M, Sunaga T, Betsuyaku S, Eto Y, Nakayashiki H, Mayama S (2001) OARE-1, a Ty1-copia retrotransposon in oat activated by abiotic and biotic stresses. Plant Cell Physiol 42:1345-1354 (Pubitemid 34067631)
30. Kloc A, Martienssen R (2008) RNAi, heterochromatin and the cell cycle. Trends Genet 24: 511-517
31. 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
32. Kubis S, Heslop-Harrison JS, Desel C, Schmidt T (1998) The genomic organization of non-LTR retrotransposons (LlNEs) from three Beta species and five other angiosperms. Plant Mol Biol 36: 821-831
33. Kumar A (1998) The evolution of plant retroviruses: moving to green pastures. Trends Plant Sci 3: 371-374
34. Kumar A, Bennetzen JL (1999) Plant retrotransposons. Annu Rev Genet 33: 479-532
35. Kuykendall D, Shao J, Trimmer K (2009) A nest of LTR retrotransposons adjacent the disease resistance-priming gene NPRl in Beta vulgaris L. U.S. Hybrid H20. Int J Plant Genomics, doi: 10.1155/2009/576742
36. Lange C, Holtgräwe D, Schulz B, Weisshaar B, Himmelbauer H (2008) Construction and characterization of a sugar beet (Beta vulgaris) fosmid library. Genome 51: 948-951
37. Laten HM, Majumdar A, Gaucher EA (1998) SIRE-I, a copfa/Tyllike retroelement from soybean, encodes a retroviral envelope-Yke protein. Proc Natl Acad. Sci USA 95: 6897-6902
38. Le Q, Melayah D, Bonnivard E, Petit M, Grandbastien MA (2007) Distribution dynamics of the Tntl retrotransposon in tobacco. Mol Genet Genomics 278: 639-651 (Pubitemid 350098275)
39. Lerat E, Capy P (1999) Retrotransposons and retroviruses: analysis of the envelope gene. Mol Biol Evol 16: 1198-1207
40. Lescot M, Dehais P, Thijs G et al (2002) PlantCARE, a database of plant cis-acting regulatory elements and a portal-tools for in silico analysis of promoter sequences. Nucleic Acids Res 30:325-327(Pubitemid 34685468)
41. Lupas A (1996) Prediction and analysis of coiled-coil structures. Methods Enzymol 266: 513-525
42. Ma J, Bennetzen JL (2004) Rapid recent growth and divergence of rice nuclear genomes. Proc Natl Acad Sci USA 101: 12404-12410 (Pubitemid 39122037)
43. Ma J, Devos KM, Bennetzen JL (2004) Analyses of LTRretrotransposon structures reveal recent and rapid genomic DNA loss in rice. Genome Res 14: 860-869 (Pubitemid 38660503)
44. Malik. HS, Henikoff S, Eickbush TH (2000) Poised for contagion: evolutionary origins of the infectious abilities of invertebrate retroviruses. Genome Res 10: 1307-1318
45. McGrath JM, Shaw RS, de los Reyes BG, Weiland JJ (2004) Construction of a sugar beet BAC library from a hybrid with diverse traits. Plant Mol Biol Report. 22: 23-28
46. Menzel G, Dechyeva D, Wenke T, Holtgräwe D, Weisshaar B, Schmidt T (2008) Diversity of a complex centromeric satellite and molecular characterization of dispersed sequence families in sugar beet (Beta vulgaris). Ann Bot 102: 521-530
47. Miguel C, Simões M, Oliveira M, Rocheta M (2008) Envelopelike retrotransposons in the plant kingdom: evidence of their presence in gymnosperms (Pinus pinaster). J Mol Evol 67: 517-525
48. Moisy C, Garrison K, Meredith C, Pelsy F (2008) Characterization of ten novel Tyl/copia-like retrotransposon families of the grapevine genome. BMC Genomics 9:469
49. Mroczek RJ, Dawe RK (2003) Distribution of retroelements in centromeres and neocentromeres of maize. Genetics 165: 809-819
50. Nagaki K, Cheng Z, Ouyang S et al (2004) Sequencing of a rice centromere uncovers active genes. Nat Genet 36: 138-145 (Pubitemid 38174371)
51. Pagni M, Ioannidis V, Cerutti L, Zahn-Zabal M, Jongeneel CV, Falquet L (2004) Myilits: a new interactive resource for protein annotation and domain identification. Nucleic Acids Res 32:W332 (Pubitemid 38997353)
52. Pearce SR (2007) SIRE-1, a putative plant retrovirus is closely related to a legume Ty1-copia retrotransposon family. Cell Mol Biol Lett 12: 120-126
53. Pearce SR, Harrison G, Li D, Heslop-Harrison JS, Kumar A, Flavell AJ (1996) The Ty1-copia group retrotransposons in Vicia species: copy number, sequence heterogeneity and chromosomal localisation. Mol Gen Genet 250: 305-315
54. Peterson-Burch BD, Voytas DF (2002) Genes of the Pseudoviridae (Ty1/copia retrotransposons). Mol Biol Evol 19: 1832-1845
55. Peterson-Burch BD, Wright DA, Laten HM, Voytas DF (2000) Retroviruses in plants? Trends Genet 16: 151-152
56. Ramallo E, Kalendar R, Schulman A, Martínez-Izquierdo J (2008) Remel, a copia retrotransposon in melon, is transcriptionally induced by UV light. Plant Mol Biol 66: 137-150
57. Rico-Cabanas L, Martínez-Izquierdo J (2007) CIRE1, a novel transcriptionally active Ty1-copia retrotransposon from Citrus sinensis. Mol Genet Genomics 277: 365-3771 (Pubitemid 46452270)
58. Saghai-Maroof MA, Soliman KM, Jorgensen RA, Allard RW (1984) Ribosomal DNA spacer-length polymorphisms in barley: mendelian inheritance, chromosomal location, and population dynamics. Proc Natl Acad Sci USA 81: 8014-8018
59. Sambrook J, Fritsch EF, Maniatis T (1989) Molecular cloning: a laboratory manual, 2nd edn. Cold Spring Harbor Laboratory Press, Cold Spring Harbor
60. SanMiguel P, Tikhonov A, Jin YK (1996) Nested retrotransposons in the intergenic regions of the maize genome. Science 274: 765-768 (Pubitemid 26398252)
61. SanMiguel P, Gaut BS, Tikhonov A, Nakajima Y, Bennetzen JL (1998) The paleontology of intergene retrotransposons of maize. Nat Genet 20: 43-45
62. Schmidt T, Heslop-Harrison JS (1998) Genomes, genes and junk: the large-scale organization of plant chromosomes. Trends Plant Sci 3: 195-199 (Pubitemid 28229040)
63. Schmidt T, Jung C, Metzlaff M (1991) Distribution and evolution of two satellite DNAs in the genus Beta. Theor Appl Genet 82: 793-799
64. Schmidt T, Schwarzacher T, Heslop-Harrison JS (1994) Physical mapping of rRNA genes by fluorescent in situ hybridization and structural analysis of 5S rRNA genes and intergenic spacer sequences in sugar beet (Betavulgaris). Theor Appl Genet 88:629-636 (Pubitemid 2133326)
65. Schmidt T, Kubis S, Heslop-Harrison JS (1995) Analysis and chromosomal localization of retrotransposons in sugar beet (Beta vulgaris L.): LINEs and. Ty1-copia-like elements as major components of the genome. Chromosome Res 3: 335-345
66. Shen Y, Ford-Lloyd BV, Newbury HJ (1998) Genetic relationships within the genus Beta determined using both PCR-based marker and DNA sequencing techniques. Heredity 80:624-632 (Pubitemid 28276302)
67. Slotkin RK, Martienssen R (2007) Transposable elements and the epigenetic regulation of the genome. Nat Rev Genet 8: 272-285 (Pubitemid 46439291)
68. Song SU, Gerasimova T, Kurkulos M, Boeke JD, Corees VG (1994) An env-like protein encoded by a Drosophila retroelement: evidence that gypsy is an infectious retrovirus. Genes Dev 8: 2046-2057
69. Tamura K, Dudley J, Nei M, Kumar S (2007) MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Mol Biol Evol 24: 1596-1599 (Pubitemid 47236692)
70. Vershinin AV, Ellis THN (1999) Heterogeneity of the internai structure of PDRl, a family of Tyl/copia-like retrotransposons in pea. Mol Gen Genet 262: 703-713
71. Wang H, Liu JS (2008) LTR retrotransposon landscape in Medicago truncatula: more rapid removal than in rice. BMC Genomics 9: 382
72. Weber B, Schmidt T (2009) Nested Ty3-gypsy retrotransposons of a single Beta procumbens centromere contain a putative chromodomain. Chromosome Res 17: 379-396
73. 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: 1072-1081 (Pubitemid 47026354)
74. Wright DA, Voytas DF (2002) Athila4 of Arabidopsis and Calypso of soybean define a lineage of endogenous plant retroviruses. Genome Res 12: 122-131
75. Wu J, Yamagata H, Hayashi-Tsugane M et al (2004) Composition and structure of the centromeric region of rice chromosome 8. Plant Cell 16: 967-976 (Pubitemid 38459216)
76. Xiong Y, Eickbush TH (1990) Origin and evolution of retroelements based upon their reverse transcriptase sequences. EMBO J 9: 3353-3362
77. Zakrzewski F, Wenke T, Holtgräwe D, Weisshaar B, Schmidt, T (2009) Analysis of a c0t-1 library enables the targeted identification of minisatellite and satellite families in Beta vulgaris. BMC Plant Biol (in press)
78. Zdobnov EM, Apweiler R (2001) InterProScan-an integration platform for the signature-recognition methods in InterPro. Bioinformatics 17: 847-848