Skip to main content
SpringerLink
Log in

Evolution and biodiversity of L1 retrotransposons in angiosperm genomes

  • Published:
Russian Journal of Genetics: Applied Research

Abstract

At present, only fragmentary data about the biodiversity and structural features of L1 retrotransposons of angiosperms related to individual elements from few genomes are available. There is no clear cladistic classification of transposable elements of this family. Structural data on elements from particular groups of angiosperm L1 retrotransposons are also scarce. For these reasons, a comprehensive structural and phylogenetic analysis of L1 retrotransposons in angiosperms has been undertaken. We have compiled information on 19 genomes of angiosperm species that was available in databases and discerned three clades of L1 elements on the base of the phylogeny of the conserved reverse transcriptase region and on their structural organization. It is demonstrated that the emergence of new protein types that form the ribonucleoprotein particles of the retrotransposons and the acquisition of RNH protein-encoding regions by several elements were crucial steps in the formation of new L1 retrotransposon types.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Similar content being viewed by others

References

  • Anisimova, M. and Gascuel, O., Approximate Likelihood-Ratio Test for Branches: A Fast, Accurate, and Powerful Alternative, Syst. Biol., 2006, vol. 55, pp. 539–552.

    Article  PubMed  Google Scholar 

  • Chaw, S.M., Chang, C.C., Chen, H.L., and Li, W.H., Dating the Monocot-Dicot Divergence and the Origin of Core Eudicots using Whole Chloroplast Genomes, J. Mol. Evol., 2004, vol. 58, pp. 424–441.

    Article  PubMed  CAS  Google Scholar 

  • Eddy, S.R., Profile Hidden Markov Models, Bioinformatics, 1998, vol. 14, pp. 755–763.

    Article  PubMed  CAS  Google Scholar 

  • Edgar, R.C., MUSCLE: Multiple Sequence Alignment with High Accuracy and High Throughput, Nucleic Acids Res., 2004, vol. 32, pp. 1792–1797.

    Article  PubMed  CAS  Google Scholar 

  • Guindon, S., Dufayard, J.F., Lefort, V., et al., New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0, Syst. Biol., 2010, vol. 59, pp. 307–321.

    Article  PubMed  CAS  Google Scholar 

  • Heitkam, T. and Schmidt, T., BNR—a LINE Family from Beta vulgaris—Contains a RRM Domain in Open Reading Frame 1 and Defines a L1 Sub-Clade Present in Diverse Plant Genomes, Plant J., 2009, vol. 59, pp. 872–882.

    Article  PubMed  CAS  Google Scholar 

  • Higashiyama, T., Noutoshi, Y., Fujie, M., and Yamada, T., Zepp, a LINE-Like Retrotransposon Accumulated in the Chlorella Telomeric Region, EMBO J., 1997, vol. 16, pp. 3715–3723.

    Article  PubMed  CAS  Google Scholar 

  • Jurka, J., Kapitonov, V.V., Pavlicek, A., et al., Repbase Update, a Database of Eukaryotic Repetitive Elements, Cytogenet. Genome Res., 2005, vol. 110, pp. 462–467.

    Article  PubMed  CAS  Google Scholar 

  • Khazina, E. and Weichenrieder, O., Non-LTR Retrotransposons Encode Noncanonical RRM Domains in Their First Open Reading Frame, Proc. Natl. Acad. Sci. U.S.A., 2009, vol. 106, pp. 731–736.

    Article  PubMed  CAS  Google Scholar 

  • Kojima, K.K. and Fujiwara, H., Cross-Genome Screening of Novel Sequence-Specific Non-LTR Retrotransposons: Various Multicopy RNA Genes and Microsatellites Are Selected as Targets, Mol. Biol. Evol., 2004, vol. 21, pp. 207–217.

    Article  PubMed  CAS  Google Scholar 

  • Kojima, K.K. and Fujiwara, H., An Extra Ordinary Retrotransposon Family Encoding Dual Endonucleases, Genome Res., 2005, vol. 15, pp. 1106–1117.

    Article  PubMed  CAS  Google Scholar 

  • Kolosha, V.O. and Martin, S.L., In vitro Properties of the First ORF Protein from Mouse LINE-1 Support Its Role in Ribonucleoprotein Particle Formation during Retrotransposition, Proc. Natl. Acad. Sci. USA, 1997, vol. 94, pp. 10155–10160.

    Article  PubMed  CAS  Google Scholar 

  • Lander, E.S., Linton, L.M., Birren, B., et al., Initial Sequencing and Analysis of the Human Genome, Nature, 2001, vol. 409, pp. 860–921.

    Article  PubMed  CAS  Google Scholar 

  • Leeton, P.R. and Smyth, D.R., An Abundant LINE-Like Element Amplified in the Genome of Lilium speciosum, Mol. Gen. Genet., 1993, vol. 237, pp. 97–104.

    Article  PubMed  CAS  Google Scholar 

  • Ma, J. and Bennetzen, J.L., Rapid Recent Growth and Divergence of Rice Nuclear Genomes, Proc. Natl. Acad. Sci. USA, 2004, vol. 101, pp. 12404–12410.

    Article  PubMed  CAS  Google Scholar 

  • Malik, H.S., Ribonuclease H Evolution in Retrotransposable Elements, Cytogenet. Genome Res., 2005, vol. 110, pp. 392–401.

    Article  PubMed  CAS  Google Scholar 

  • Marchler-Bauer, A., Lu, S., Anderson, J.B., et al., CDD: a Conserved Domain Database for the Functional Annotation of Proteins, Nucleic Acids Res., 2011, vol. 39, pp. 225–229.

    Article  Google Scholar 

  • Maris, C., Dominguez, C., and Allain, F.H., The RNA Recognition Motif, a Plastic RNA-Binding Platform to Regulate Post-Transcriptional Gene Expression, FEBSJ, 2005, vol. 272, pp. 2118–2131.

    Article  CAS  Google Scholar 

  • Martin, S.L., The ORF1 Protein Encoded by LINE-1: Structure and Function during L1 Retrotransposition, J. Biomed. Biotechnol, 2006.

  • Matsui, T., Tanaka, T., Endoh, H., et al., The RNA Recognition Mechanism of Human Immunodeficiency Virus (HIV) Type 2 NCp8 Is Different from that of HIV-1 NCp7, Biochemistry, 2009, vol. 48, pp. 4314–4323.

    Article  PubMed  CAS  Google Scholar 

  • Noma, K., Ohtsubo, E., and Ohtsubo, H., Non-LTR Retrotransposons (LINEs) as Ubiquitous Components of Plant Genomes, Mol. Gen. Genet., 1999, vol. 261, pp. 71–79.

    Article  PubMed  CAS  Google Scholar 

  • Noma, K., Ohtsubo, H., and Ohtsubo, E., ATLN Elements, LINEs from Arabidopsis thaliana: Identification and Characterization, DNA Res., 2000, vol. 7, pp. 291–303.

    Article  PubMed  CAS  Google Scholar 

  • Novikova, O., Fet, V., and Blinov, A., Non-LTR Retrotransposons in Fungi, Funct. Integr. Genomics, 2008, vol. 9, pp. 27–42.

    Article  PubMed  Google Scholar 

  • Rho, M., Tang H. MGE Scannon-LTR: Computational Identification and Classification of Autonomous Non-LTR Retrotransposons in Eukaryotic Genomes, Nucleic Acids Res., 2009, vol. 37, p. e143.

    Article  PubMed  Google Scholar 

  • Sakamoto, K., Ohmido, N., Fukui, K., et al., Site-Specific Accumulation of a LINE-Like Retrotransposon in a Sex Chromosome of the Dioecious Plant Cannabis sativa, Plant. Mol. Biol., 2000, vol. 44, pp. 723–732.

    Article  PubMed  CAS  Google Scholar 

  • Schwarz-Sommer, Z., Leclercq, L., Gobel, E., and Saedler, H., Cin4, An Insert Altering the Structure of the A1 Gene in Zea mays, Exhibits Properties of Nonviral Retrotransposons, EMBO J., 1987, vol. 6, pp. 3873–3880.

    PubMed  CAS  Google Scholar 

  • Sding, J., Protein Homology Detection by HMM-HMM Comparison, Bioinformatics, 2005, vol. 21, pp. 951–960.

    Article  Google Scholar 

  • Sergeeva, E.M. and Salina, E.A., Mobile Elements and the Evolution of the Plant Genome, Vavilov. Zh. Genet. Selekts., 2011, vol. 15, no. 2, pp. 382–398.

    Google Scholar 

  • Sormacheva, N.D. and Blinov, A.G., LTR Retrotransposons of Plants, Vavilov. Zh. Genet. Selekts., 2011, vol. 15, no. 2, pp. 351–381.

    Google Scholar 

  • Tamura, K., Peterson, D., Peterson, N., et al., MEGA5: Molecular Evolutionary Genetics Analysis Using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods, Mol. Biol. Evol., 2011. http://www.kumarlab.net/publications

  • Turcotte, K., Srinivasan, S., and Bureau, T., Survey of Transposable Elements from Rice Genomic Sequences, Plant J., 2001, vol. 25, pp. 169–179.

    Article  PubMed  CAS  Google Scholar 

  • Vershinin, A.V., Druka, A., Alkhimova, A.G., et al., LINEs and gypsy-Like Retrotransposons in Hordeum Species, Plant. Mol. Biol., 2002, vol. 49, pp. 1–14.

    Article  PubMed  CAS  Google Scholar 

  • Wenke, T., Holtgrwe, D., Horn, A.V., et al., An Abundant and Heavily Truncated Non-LTR Retrotransposon (LINE) Family in Beta vulgaris, Plant. Mol. Biol., 2009, vol. 71, pp. 585–597.

    Article  PubMed  CAS  Google Scholar 

  • Wright, D.A., Ke, N., Smalle, J., et al., Multiple Non-LTR Retrotransposons in the Genome of Arabidopsis thaliana, Genetics, 1996, vol. 142, pp. 569–578.

    PubMed  CAS  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Novosibirsk State University, Novosibirsk, Russia

    G. A. Smyshlyaev

  2. Institute of Cytology and Genetics, Siberian Branch, Russian Academy of Sciences, Novosibirsk, Russia

    A. G. Blinov

Authors
  1. G. A. Smyshlyaev
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. A. G. Blinov
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to G. A. Smyshlyaev.

Additional information

Original Russian Text © G.A. Smyshlyaev, A.G. Blinov, 2011, published in Vavilovskii Zhurnal Genetiki i Selektsii, 2011, Vol. 15, No. 3, pp. 563–571.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Smyshlyaev, G.A., Blinov, A.G. Evolution and biodiversity of L1 retrotransposons in angiosperm genomes. Russ J Genet Appl Res 2, 72–78 (2012). https://doi.org/10.1134/S2079059712010133

Download citation

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1134/S2079059712010133

Keywords

Search

Navigation