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Isolation and characterization of genomic retrotransposon sequences from octoploid strawberry (Fragaria × ananassa Duch.)

  • Genetic Transformation and Hybridization
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Abstract

Strawberry (Fragaria spp.) is a kind of herbaceous perennial plant that propagates vegetatively. The conserved domains of reverse transcriptase (RT) genes of Ty1-copia and Ty3-gypsy groups of LTR retrotransposons were amplified from the cultivated strawberry (Fragaria × ananassa Duch.). Sequence analysis of clones demonstrated that 5 of 19 Ty1-copia group unique sequences and 2 of 10 Ty3-gypsy unique sequences in F. × ananassa genome possessed either stop codon or frameshift. Ty1-copia group sequences are highly heterogeneous (divergence ranged from 1 to 69.8%), but the Ty3-gypsy group sequences are less (divergence ranged from 1 to 10%). Southern dot blot hybridization result suggested that both of the LTR retrotransposons are present in the genome of cultivated strawberry with high copy number (Ty1-copia group 2,875 Ty3-gypsy group 348). RT-PCR amplification from total RNA, which was extracted from leaves of micropropagated strawberry plants, did not yield either of the RT fragments. This is the first report on the presence of RT sequences of Ty1-copia and Ty3-gypsy group retrotransposons in F. × ananassa genome.

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Abbreviations

LTR :

Long terminal repeat

PCR :

Polymerase chain reaction

RT :

Reverse transcriptase

TE :

Transposable element

RT-PCR :

Reverse transcription polymerase chain reaction

S-SAP :

Sequence-specific amplification polymorphism

References

  • Asíns MJ, Monforte AJ, Mestre PF, Carbonell EA (1999) Citrus and Prunus copia-like retrotransposons. Theor Appl Genet 99:503–510

    Article  Google Scholar 

  • Beguiristain T, Grandbastien MA, Puigdomenech P, Casacuberta JM (2001) Three Tnt1 subfamilies show different stress-associated patterns of expression in tobacco. Consequences for retrotransposon control and evolution in plants. Plant Physiol 127:212–221

    Article  PubMed  CAS  Google Scholar 

  • Bennetzen JL (2002) Mechanisms and rates of genome expansion and contraction in flowering plants. Genetica 115:29–36

    Article  PubMed  CAS  Google Scholar 

  • Bernet GP, Asíns MJ (2003) Identification and genomic distribution of gypsy like retrotransposons in Citrus and Poncirus. Theor Appl Genet 108:121–130

    Article  PubMed  CAS  Google Scholar 

  • Casacuberta JM, Santiago N (2003) Plant LTR-retro-transposons and MITEs: control of transposition and impact on the evolution of plant genes and genomes. Gene 311:1–11

    Article  PubMed  CAS  Google Scholar 

  • Chang L, Zhang Z, Yang H, Li H, Dai H (2007) Detection of strawberry RNA and DNA viruses by RT-PCR using total nucleic acid as a template. J Phytopathol 155:431–436

    Article  CAS  Google Scholar 

  • Charlesworth B (1986) Genetic divergence between transposable elements. Genet Res 48:111–118

    Article  PubMed  CAS  Google Scholar 

  • Dai H, Zhang Z, Guo X (2007) Adventitious bud regeneration from leaf and cotyledon explants of Chinese hawthorn (Crataegus pinnatifida Bge. var. major N.E.Br.). In Vitro Cell Dev Biol Plant 43:2–8

    CAS  Google Scholar 

  • Echenique V, Stamova B, Wolters P, Lazo G, Carollo VL, Dubcovsky J (2002) Frequencies of Ty1-copia and Ty3-gypsy retroelements within the Triticeae EST databases. Theor Appl Genet 104:840–844

    Article  PubMed  CAS  Google Scholar 

  • Flavell AJ (1999) Long terminal repeat retrotransposons jump between species. Proc Natl Acad Sci USA 96:12211–12212

    Article  PubMed  CAS  Google Scholar 

  • Flavell AJ, Dunbar E, Anderson R, Pearce SR, Hartley R, Kumar A (1992a) Ty1-copia group retrotransposons are ubiquitous and heterogeneous in higher plants. Nucleic Acids Res 20:3639–3644

    Article  PubMed  CAS  Google Scholar 

  • Flavell AJ, Smith DB, Kumar A (1992b) Extreme heterogeneity of Ty1-copia group retrotransposons in plants. Mol Gen Genet 231:233–242

    PubMed  CAS  Google Scholar 

  • Friesen N, Brandes A, Heslop-Harrison (2001) Diversity, origin and distribution of retrotransposons (gypsy and copia) in conifers. Mol Biol Evol 18:1176–1188

    PubMed  CAS  Google Scholar 

  • 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

    Article  PubMed  CAS  Google Scholar 

  • Grandbastien MA (1992) Retroelements in higher plants. Trends Genet 8:103–108

    PubMed  CAS  Google Scholar 

  • Grandbastien MA, Spielmann A., Caboche M (1989) Tnt1, a mobile retroviral-like transposable element of tobacco isolated by plant cell genetics. Nature 337:376–380

    Article  PubMed  CAS  Google Scholar 

  • Hill P, Burford D, Martin DMA, Flavell AJ (2005) Retrotransposon populations of Vicia species with varying genome size. Mol Genet Genomics 273:371–381

    Article  PubMed  CAS  Google Scholar 

  • Hirochika H, Hirochika R (1993) Ty1-copia group retrotransposons as ubiquitous components of plant genomes. Jpn J Genet 68:35–46

    Article  PubMed  CAS  Google Scholar 

  • Hirochika H, Fukuchi A, Kikuchi F (1992) Retrotransposon families in rice. Mol Gen Genet 233:209–216

    Article  PubMed  CAS  Google Scholar 

  • Hirochika H, Otsuki H, Yoshikawa M, Otsuki Y, Sugimoto K, Takeda S (1996a) Autonomous transposition of the tobacco retrotransposon Tto1 in rice. Plant Cell 8:725–734

    Article  PubMed  CAS  Google Scholar 

  • Hirochika H, Sugimoto K, Otsuki Y, Tsugawa H, Kanda M (1996b) Retrotransposons of rice involved in mutations induced by tissue culture. Proc Natl Acad Sci USA 93:7783–7788

    Article  PubMed  CAS  Google Scholar 

  • Jordan IK, Matyunina LV, McDonald JF (1999) Evidence for the recent horizontal transfer of long terminal repeat retrotransposon. Proc Natl Acad Sci USA 96:12621–12625

    Article  PubMed  CAS  Google Scholar 

  • 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

    Article  PubMed  CAS  Google Scholar 

  • Kidwell MG, Lisch D (1997) Transposable elements as sources of variation in animals and plants. Proc Natl Acad Sci USA 94:7704–7711

    Article  PubMed  CAS  Google Scholar 

  • 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

    Article  PubMed  CAS  Google Scholar 

  • Kinet JM, Parmentier A (1989) The flowering behaviour of micropropagated strawberry plants cv. ‘Gorella’: the influence of the number of sub-cultures on the multiplication medium. Acta Hortic 265:327–334

    Google Scholar 

  • Kobayashi S, Goto-Yamamoto N, Hirochika H (2004) Retrotransposon-induced mutations in grape skin color. Science 304:982

    Article  PubMed  Google Scholar 

  • Kubis SE, Castilho AM, Vershinin AV, Heslop-Harrison JS (2003) Retroelements, transposons and methylation status in the genome of oil palm (Elaeis guineensis) and the relationship to somaclonal variation. Plant Mol Biol 52:69–79

    Article  PubMed  CAS  Google Scholar 

  • Kumar A, Bennetzen JL (1999) Plant retrotransposons. Annu Rev Genet 33:479–532

    Article  PubMed  CAS  Google Scholar 

  • Kumar A, Pearce SR, McLean K, Harrison G, Heslop-Harrison JS, Waugh R, Flavell AJ (1997) The Ty1-copia group of retrotransposons in plants: genomic organisation, evolution and use as molecular markers. Genetica 100:205–217

    Article  PubMed  CAS  Google Scholar 

  • Kumar S, Tamura K, Nei M (2004) MEGA3: integrated software for molecular evolutionary genetics analysis and sequence alignment. Brief Bioinform 5:150–163

    Article  PubMed  CAS  Google Scholar 

  • Kumekawa N, Ohtsubo E, Ohtsubo H (1999) Identification and phylogenetic analysis of gypsy-type retrotransposons in the plant kingdom. Genes Genet Syst 74:299–307

    Article  PubMed  CAS  Google Scholar 

  • Lodhi MA, Ye GN, Weeden NF, Reisch BI (1994) A simple and efficient method for DNA extraction from grapevine cultivars Vitis species and Ampelopsis. Plant Mol Bio Rep 12:6–13

    Article  CAS  Google Scholar 

  • Ma J, Bennetzen JL (2004) Rapid recent growth and divergence of rice nuclear genomes. Proc Natl Acad Sci USA 101:12404–12410

    Article  PubMed  CAS  Google Scholar 

  • MacRae AF (1998) A pentamer-repeat-containing DNA sequence in Texas bluebonnet (Lupinus texensis Hook.). Genome 41:553–559

    Article  PubMed  CAS  Google Scholar 

  • Matsuoka Y, Tsunewaki K (1996) Wheat retrotransposon families identified by reverse transcriptase domain analysis. Mol Biol Evol 13:1384–1392

    PubMed  CAS  Google Scholar 

  • Moore PP, Robbins JA, Sjulin TM (1991) Field performance of Olympus strawberry subclones. J AM Soc Hortic Sci 26:192–194

    Google Scholar 

  • Murashige T, Skoog F (1962) A revised medium for rapid growth and bioassays with tobacco tissue culture. Physiol Plant 15:473–497

    Article  CAS  Google Scholar 

  • Muthukumar B, Bennetzen JL (2004) Isolation and characterization of genomic and transcribed retrotransposon sequences from sorghum. Mol Genet Genomics 271:308–316

    Article  PubMed  CAS  Google Scholar 

  • Nehra NS, Kartha KK, Stushnoff C (1991) Nuclear DNA content and isozyme variation in relation to morphogenic potential of Strawberry (Fragaria x ananassa) callus cultures. Can J Bot 69:239–244

    Article  CAS  Google Scholar 

  • Nicholas KB, Nicholas HB (1997). http://www.psc.edu/biomed/genedoc

  • Pearce SR, Harrison G, Li D, Heslop-Harrison JS, Kumar A, Flavell AJ (1996a) The Ty1-copia group retrotransposons in Vicia species: copy number, sequence heterogeneity and chromosomal localisation. Mol Gen Genet 250:305–315

    PubMed  CAS  Google Scholar 

  • Pearce SR, Kumar A, Flavell AJ (1996b) Activation of the Ty1-copia group retrotransposons of potato (Solanum tuberosum) during protoplast isolation. Plant Cell Rep 15:949–953

    Article  CAS  Google Scholar 

  • Pouteau S, Grandbastien MA, Boccara M (1994) Microbial elicitors of plant defense responses activate transcription of a retrotransposon. Plant J 5:535–542

    Article  CAS  Google Scholar 

  • Pouteau S, Huttner E, Grandbastien MA, Caboche M (1991) Specific expression of the tobacco Tnt1 retrotransposon in protoplasts. EMBO J 10:1911–1918

    PubMed  CAS  Google Scholar 

  • SanMiguel P, Tikhonov A, Jin YK, Motchoulskaia N, Zakharov D, Melake-Berhan A, Springer PS, Edwards KJ, Lee M, Avramova Z, Bennetzen JL. (1996) Nested retrotransposons in the intergenic regions of the maize genome. Science 273:765–769

    Article  Google Scholar 

  • Sant VJ, Sainani MN, Sami-subbu R, Ranjekar PK, Gupta VS (2000) Ty1-copia retrotransposon-like elements in chickpea genome: their identification, distribution and use for diversity analysis. Gene 257:157–166

    Article  PubMed  CAS  Google Scholar 

  • Santini S, Cavallini A, Natali L, Minelli S, Maggini F, Cionini PG (2002) Ty1-copia-like and Ty3-gypsy-like DNA sequence in Helianthus species. Chromosoma 111:192–200

    Article  PubMed  CAS  Google Scholar 

  • Silva JC, Loreto EL, Clark Jonathan BC (2004) Factors that affect the horizontal transfer of transposable elements. Curr Issues Mol Biol 6:57–72

    PubMed  CAS  Google Scholar 

  • Su PY, Brown TA (1997) Ty3-gypsy-like retrotransposon sequences in tomato. Plasmid 38:148–157

    Article  PubMed  CAS  Google Scholar 

  • Swartz HJ, Galletta GJ, Zimmerman RH (1981) Field performance and phenotypic stability of tissue culture-propagated strawberries. J Am Soc Hortic Sci 106:667–673

    Google Scholar 

  • Tahara M, Aoki T, Suzuka S, Yamashita H, Tanaka M, Matsunaga S, Kokumai S (2004) Isolation of an active element from a high-copy-number family of retrotransposons in the sweetpotato genome. Mol Gen Genomics 272:116–127

    Article  CAS  Google Scholar 

  • Takeda S, Sugimoto K, Otsuki H, Hirochika H (1998) Transcriptional activation of the tobacco retrotransposon Tto1 by wounding and methyl jasmonate. Plant Mol Biol 36:365–376

    Article  PubMed  CAS  Google Scholar 

  • Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG (1997) The CLUSTAL X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 25:4876–4882

    Article  PubMed  CAS  Google Scholar 

  • Villordon AQ, Jarret RL, Labonte DR (2000) Detection of Ty1-copia-like reverse transcriptase sequences in Ipomoea batatas (L.) Poir. Plant Cell Rep 19:1219–1225

    Article  CAS  Google Scholar 

  • Waugh R, McLean K, Flavell AJ, Pearce SR, Kumar A, Thomas BBT, Powell W (1997) Genetic distribution of Bare-1-like retrotransposable elements in the barley genome revealed by sequence-specific amplification polymorphisms (S-SAP). Mol Gen Genet 253:687–694

    Article  PubMed  CAS  Google Scholar 

  • Wessler SR, Bureau TE, White SE (1995) LTR-retrotransposons and MITEs: important players in the evolution of plant genomes. Curr Opin Genet Dev 5:814–821

    Article  PubMed  CAS  Google Scholar 

  • Wilhelm M, Whilhem FX (2001) Reverse transcription of retroviruses and LTR retrotransposons. Cell Mol Life Sci 58:1246–1262

    Article  PubMed  CAS  Google Scholar 

  • Yanez M, Verdugo I, Rodriguez M, Prat S, Ruiz-Lara S (1998) Highly heterogeneous families of Ty1/copia retrotransposons in the Lycopersicon chilense genome. Gene 222:223–228

    Article  PubMed  CAS  Google Scholar 

  • Yao JL, Dong YH, Bret AM (2001) Parthenocarpic apple fruit production conferred by transposon insertion mutations in a MADS-box transcription factor. Plant Biol 98:1306–1311

    CAS  Google Scholar 

  • Zaki EA, Abdel Ghany AA (2004) Ty3-gypsy Retro-Transposons in Egyptian cotton (G. barbadense). J Cott Sci 8:179–185

    CAS  Google Scholar 

Download references

Acknowledgments

This work was supported by National Natural Science Foundation of China (Grant No. 30671432), Program for New Century Excellent Talents in University (NCET) and Science Foundation of Department of Education from Liaoning Province.

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Authors and Affiliations

  1. College of Horticulture, Shenyang Agricultural University, Dongling Road 120, Shenyang, 110161, People’s Republic of China

    Yue Ma, Haiyue Sun, Guiling Zhao, Hongyan Dai, Xiuyan Gao, He Li & Zhihong Zhang

  2. Key Laboratory of Agricultural Biotechnology of Liaoning Province, Dongling Road 120, Shenyang, 110161, People’s Republic of China

    Zhihong Zhang

  3. College of Forestry, Shenyang Agricultural University, Dongling Road 120, Shenyang, 110161, People’s Republic of China

    Guiling Zhao

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  1. Yue Ma
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  2. Haiyue Sun
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Correspondence to Zhihong Zhang.

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Communicated by R. Reski.

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Ma, Y., Sun, H., Zhao, G. et al. Isolation and characterization of genomic retrotransposon sequences from octoploid strawberry (Fragaria × ananassa Duch.). Plant Cell Rep 27, 499–507 (2008). https://doi.org/10.1007/s00299-007-0476-7

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  • DOI: https://doi.org/10.1007/s00299-007-0476-7

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