Identification and characterization of jute LTR retrotransposons

References

• Ma Y, Sun H, Zhao G, Dai H, Gao X, Li H, et al. Isolation and characterization of genomic retrotransposon sequences from octoploid strawberry (Fragaria x ananassa Duch.). Plant Cell Rep 2008; 27:499 - 507
   PubMed Web of Science ®Google Scholar
• Kumar A, Bennetzen JL. Plant retrotransposons. Annu Rev Genet 1999; 33:479 - 532
   PubMed Web of Science ®Google Scholar
• SanMiguel P, Tikhonov A, Jin YK, Motchoulskaia N, Zakharov D, Melake-Berhan A, et al. Nested retrotransposons in the intergenic regions of the maize genome. Science 1996; 274:765 - 768
   PubMed Web of Science ®Google Scholar
• Rico-Cabanas L, Martinez-Izquierdo JA. CIRE1, a novel transcriptionally active Ty1-copia retrotransposon from Citrus sinensis. Mol Genet Genomics 2007; 277:365 - 377
   PubMed Web of Science ®Google Scholar
• Tang YM, Ma YZ, Li LC, Ye XG. Identification and Characterization of Reverse Transcriptase Domain of Transcriptionally Active Retrotransposons in Wheat Genomes. J Integr Plant Biol 2005; 47:604 - 612
   Web of Science ®Google Scholar
• Wilhelm M, Wilhelm FX. Reverse transcription of retroviruses and LTR retrotransposons. Cell Mol Life Sci 2001; 58:1246 - 1262
   PubMed Web of Science ®Google Scholar
• Wessler SR, Bureau TE, White SE. LTR-retrotransposons and MITEs: important players in the evolution of plant genomes. Curr Opin Genet Dev 1995; 5:814 - 821
   PubMed Web of Science ®Google Scholar
• Vitte C, Panaud O. LTR retrotransposons and flowering plant genome size: emergence of the increase/decrease model. Cytogenet Genome Res 2005; 110:91 - 107
   PubMed Web of Science ®Google Scholar
• Grandbastien MA. Activation of plant retrotransposons under stress conditions. Trends in Plant Science 1998; 3:181 - 187
   Web of Science ®Google Scholar
• Su PY, Brown TA. Ty3/gypsy-like retrotransposon sequences in tomato. Plasmid 1997; 38:148 - 157
   PubMed Web of Science ®Google Scholar
• Zaki E, Ghany A. Ty3-gypsy Retro-Transposons in Egyptian cotton (G. barbadense). Journal of Cotton Science 2004; 8:179 - 185
   Google Scholar
• Purugganan MD, Wessler SR. Molecular evolution of magellan, a maize Ty3/gypsy-like retrotransposon. Proc Natl Acad Sci USA 1994; 91:11674 - 11678
   PubMed Web of Science ®Google Scholar
• Ma J, Bennetzen JL. Rapid recent growth and divergence of rice nuclear genomes. Proc Natl Acad Sci USA 2004; 101:12404 - 12410
   PubMed Web of Science ®Google Scholar
• Vitte C, Panaud O, Quesneville H. LTR retrotransposons in rice (Oryza sativa, L.): recent burst amplifications followed by rapid DNA loss. BMC Genomics 2007; 8:218
   PubMed Web of Science ®Google Scholar
• Monsour A. Epigenetic activation of genomic retrotransposons. J Cell Mol Biol 2007; 6:99 - 107
   Google Scholar
• Ahmed S, Nabi Z, Alam MM, Islam MS, Samira R, Moosa MM, et al. A computational and experimental approach for developing jute ESTs from genomic clones. Australian Journal of Crop Science 2009; 3:322 - 328
   Web of Science ®Google Scholar
• Wicker T, Sabot F, Hua-Van A, Bennetzen JL, Capy P, Chalhoub B, et al. A unified classification system for eukaryotic transposable elements. Nat Rev Genet 2007; 8:973 - 982
   PubMed Web of Science ®Google Scholar
• Sun HY, Dai HY, Zhao GL, Ma Y, Ou CQ, Li H, et al. Genome-wide characterization of long terminal repeat—retrotransposons in apple reveals the differences in heterogeneity and copy number between Ty1-copia and Ty3-gypsy retrotransposons. J Integr Plant Biol 2008; 50:1130 - 1139
   PubMed Web of Science ®Google Scholar
• Samad MA, Kabir G, Islam AS. Interphase nuclear structure and heterochromatin in two species of Corchorus and their F[1] hybrid. Cytologia 1992; 57:21 - 25
   Google Scholar
• Hill P, Burford D, Martin DM, Flavell AJ. Retrotransposon populations of Vicia species with varying genome size. Mol Genet Genomics 2005; 273:371 - 381
   PubMed Web of Science ®Google Scholar
• Brandes A, Heslop-Harrison JS, Kamm A, Kubis S, Doudrick RL, Schmidt T. Comparative analysis of the chromosomal and genomic organization of Ty1-copia-like retrotransposons in pteridophytes, gymnosperms and angiosperms. Plant Mol Biol 1997; 33:11 - 21
   PubMed Web of Science ®Google Scholar
• Flavell AJ, Dunbar E, Anderson R, Pearce SR, Hartley R, Kumar A. Ty1-copia group retrotransposons are ubiquitous and heterogeneous in higher plants. Nucleic Acids Res 1992; 20:3639 - 3644
   PubMed Web of Science ®Google Scholar
• Sant VJ, Sainani MN, Sami-Subbu R, Ranjekar PK, Gupta VS. Ty1-copia retrotransposon-like elements in chickpea genome: their identification, distribution and use for diversity analysis. Gene 2000; 257:157 - 166
   PubMed Web of Science ®Google Scholar
• Santini, Cavallini, Natali, Minelli, Maggini, Cionini. Ty1-copia-like and Ty3-gypsy-like DNA sequence in Helianthus species. Chromosoma 2002; 111:192 - 200
   PubMed Web of Science ®Google Scholar
• Voytas DF, Cummings MP, Koniczny A, Ausubel FM, Rodermel SR. copia-like retrotransposons are ubiquitous among plants. Proc Natl Acad Sci USA 1992; 89:7124 - 7128
   PubMed Web of Science ®Google Scholar
• Hirochika H, Hirochika R. Ty1-copia group retrotransposons as ubiquitous components of plant genomes. Jpn J Genet 1993; 68:35 - 46
   PubMedGoogle Scholar
• Tao NG, Xu J, Cheng YJ, Hong L, Guo W-W, Yi HL, et al. Isolation and Characterization of Copia-like Retrotransposons from 12 Sweet Orange (Citrus sinensis Osbeck) Cultivars. J Integr Plant Biol 2005; 47:1507 - 1515
   Web of Science ®Google Scholar
• Muthukumar B, Bennetzen JL. Isolation and characterization of genomic and transcribed retrotransposon sequences from sorghum. Mol Genet Genomics 2004; 271:308 - 316
   PubMed Web of Science ®Google Scholar
• Avramova Z, SanMiguel P, Georgieva E, Bennetzen JL. Matrix Attachment Regions and Transcribed Sequences within a Long Chromosomal Continuum Containing Maize Adh1. Plant Cell 1995; 7:1667 - 1680
   PubMed Web of Science ®Google Scholar
• Dixit A, Ma KH, Yu JW, Cho EG, Park YJ. Reverse transcriptase domain sequences from Mungbean (Vigna radiata) LTR retrotransposons: sequence characterization and phylogenetic analysis. Plant Cell Rep 2006; 25:100 - 111
   PubMed Web of Science ®Google Scholar
• Domingo E, Holland J. Morse SS. Mutation rates and rapid evolution of RNA viruses. The Evolutionary Biology of Viruses 1994; New York Raven Press 161 - 164
   Google Scholar
• Charlesworth B. Genetic divergence between transposable elements. Genet Res (Camb) 1986; 48:111 - 118
   Google Scholar
• Heslop-Harrison JS, Brandes A, Taketa S, Schmidt T, Vershinin AV, Alkhimova EG, et al. The chromosomal distributions of Ty1-copia group retrotransposable elements in higher plants and their implications for genome evolution. Genetica 1997; 100:197 - 204
   PubMed Web of Science ®Google Scholar
• Liu B, Piao H, Zhao F, Zhao J, Liu Z, Huang B. DNA Methylation Changes in Rice Induced by Zizania Latifolia (Griseb.) DNA Introgression. Hereditas 1999; 131:75 - 78
   Web of Science ®Google Scholar
• Springer MS, Davidson EH, Britten RJ. Retroviral-like element in a marine invertebrate. Proc Natl Acad Sci USA 1991; 88:8401 - 8404
   PubMed Web of Science ®Google Scholar
• Springer MS, Tusneem NA, Davidson EH, Britten RJ. Phylogeny, rates of evolution and patterns of codon usage among sea urchin retroviral-like elements, with implications for the recognition of horizontal transfer. Mol Biol Evol 1995; 12:219 - 230
   PubMed Web of Science ®Google Scholar
• McAllister BF, Werren JH. Phylogenetic analysis of a retrotransposon with implications for strong evolutionary constraints on reverse transcriptase. Mol Biol Evol 1997; 14:69 - 80
   PubMed Web of Science ®Google Scholar
• Meyers BC, Tingey SV, Morgante M. Abundance, distribution and transcriptional activity of repetitive elements in the maize genome. Genome Res 2001; 11:1660 - 1676
   PubMed Web of Science ®Google Scholar
• Navarro-Quezada A, Schoen DJ. Sequence evolution and copy number of Ty1-copia retrotransposons in diverse plant genomes. Proc Natl Acad Sci USA 2002; 99:268 - 273
   PubMed Web of Science ®Google Scholar
• Cavalier-Smith T. Nuclear volume control by nucleoskeletal DNA, selection for cell volume and cell growth rate, and the solution of the DNA C-value paradox. J Cell Sci 1978; 34:247 - 278
   PubMed Web of Science ®Google Scholar
• Todorovska E. Retrotransposons and their role in plant-genome evolution. Biotechnol & Biotechnol Eq 2007; 21:294 - 305
   Web of Science ®Google Scholar
• Suoniemi A, Narvanto A, Schulman AH. The BARE-1 retrotransposon is transcribed in barley from an LTR promoter active in transient assays. Plant Mol Biol 1996; 31:295 - 306
   PubMed Web of Science ®Google Scholar
• Grandbastien MA, Lucas H, Morel JB, Mhiri C, Vernhettes S, Casacuberta JM. The expression of the tobacco Tnt1 retrotransposon is linked to plant defense responses. Genetica 1997; 100:241 - 252
   PubMed Web of Science ®Google Scholar
• Tahara M, Aoki T, Suzuka S, Yamashita H, Tanaka M, Matsunaga S, et al. Isolation of an active element from a high-copy-number family of retrotransposons in the sweetpotato genome. Mol Genet Genomics 2004; 272:116 - 127
   PubMed Web of Science ®Google Scholar
• Feschotte C, Jiang N, Wessler SR. Plant transposable elements: where genetics meets genomics. Nat Rev Genet 2002; 3:329 - 341
   PubMed Web of Science ®Google Scholar
• Berenyi M, Gichuki T, Schmidt J, Burg K. Ty1-copia retrotransposon-based S-SAP (sequence-specific amplified polymorphism) for genetic analysis of sweetpotato. Theor Appl Genet 2002; 105:862 - 869
   PubMed Web of Science ®Google Scholar
• Chadha S, Gopalakrishna T. Comparative assessment of REMAP and ISSR marker assays for genetic polymorphism studies in Magnaporthe grisea. Current Science 2007; 93:688 - 692
   Web of Science ®Google Scholar
• Haque S, Ashraf N, Awal A, Sarker R, Begum S, Khan H. Method for Quality DNA Isolation from Different Parts of Jute Plant: Corchorus capsularis L. and C. olitorius L.. Plant Tissue Cult 2004; 14:143 - 148
   Google Scholar
• Flavell AJ, Smith DB, Kumar A. Extreme heterogeneity of Ty1-copia group retrotransposons in plants. Mol Gen Genet 1992; 231:233 - 242
   PubMedGoogle Scholar
• Winstanley C, Rapley R. The Nucleic Acid Protocols Handbook: Extraction and Purification of Plasmid DNA 2000; Totowa Humana Press Inc
   Google Scholar
• Llorens C, Futami R, Bezemer D, Moya A. The Gypsy Database (GyDB) of mobile genetic elements. Nucleic Acids Res 2008; 36:38 - 46
   Web of Science ®Google Scholar
• Tamura K, Dudley J, Nei M, Kumar S. MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Mol Biol Evol 2007; 24:1596 - 1599
   PubMed Web of Science ®Google Scholar
• Sanderson MJ. Confidence limits on phylogenies: the bootstrap revisited. Cladistics 1989; 5:113 - 129
   PubMed Web of Science ®Google Scholar
• Nei M, Gojobori T. Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions. Mol Biol Evol 1986; 3:418 - 426
   PubMed Web of Science ®Google Scholar