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Sequence heterogeneity of theenvelope-like domain in cultivated allotetraploidGossypium species and their diploid progenitors

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Abstract

Retroviralenvelope (env)-like sequences in 2 cultivated allotetraploid cottons and their diploid progenitors have been identified and characterized in this study. DNA sequence analysis reveals that these sequences are heterogeneous. The observed sequence diversity, however, seems to preserve coding information. This is evidenced by the detection of the transmembrane domain (TM), which is the most conserved feature of the divergent retroviral env genes. The high ratio of synonymous to nonsynonymous changes suggests that these sequences are evolving under purifying selection. Phylogenetic analysis shows thatGossypium sequences closely cluster with a lineage of plant endogenous retroviruses that have anenv-like gene. These results provide evidence for the antiquity and the wide diversity ofenv-like sequences in theGossypium genome.

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References

  • Abdel Ghany AA, Zaki EA, 2002. Cloning and sequencing of an envelope-like gene inGossypium. Planta 216: 351–353.

    Article  CAS  PubMed  Google Scholar 

  • Abdel Ghany AA, Zaki EA, 2003. Sequence heterogeneity of the envelope-like domain in the Egyptian cottonGossypium barbadense. Afr J Biotech 2: 341–44.

    CAS  Google Scholar 

  • Abdel Ghany AA, Zaki EA, 2005. Isolation, characterization, and phylogenetic analysis of Bagy-2 retrotransposon envelope-domain in the Egyptian cottonG. barbadense. A J Biotech 8: 115–126.

    Google Scholar 

  • Boeke JD, Eickbush TH, Sandmeyer SB, Voytas DF, 2000. Metaviridae. In: Murphy FA, ed. Virus taxonomy: ICTV VIIth Report, Springer, New York, 124–135.

    Google Scholar 

  • Capy P, 2005. Classification and nomenclature of retrotransposable elements. Cytogenet Genome Res 110: 457–461.

    Article  CAS  PubMed  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  CAS  PubMed  Google Scholar 

  • Chavanne F, Zhang DX, Liaud MF, Cerff R, 1998. Structure and evolution of Ty3/Gypsy family highly amplified in pea and other legume species. Plant Mol Biol 37: 363–375.

    Article  CAS  PubMed  Google Scholar 

  • Eickbush TH, Malik HS, 2002. Origins and evolution of retrotransposons. In: Craig NL, Craigie R, Gellert M, Lambowitz AM, eds. Mobile DNA II. ASM Press, Washington, D.C: 1111–1144.

    Google Scholar 

  • Grandbastien MA, Lucas H, Morel JB, Mhiri C, Vernhettes S, Casacuberta TM, 1997. The expression of the tobacco Tnt1 retrotransposon is linked to plant defense responses. Genetica 100: 241–52.

    Article  CAS  PubMed  Google Scholar 

  • Hawkins JS, Kim H, Nason JD, Wing RA, Wendel JF, 2006. Differential lineage-specific amplification of transposable elements is responsible for genome size variation inGossypium. Genome Res 16: 1252–1261.

    Article  CAS  PubMed  Google Scholar 

  • Hirokawa T, Boon-Chieng S, Mitaku S, 1998. SOSUI: classification and secondary structure prediction system for membrane proteins. Bioinformatics 14: 378–79.

    Article  CAS  PubMed  Google Scholar 

  • Hofmann K, Stoffel W, 1993. TMbase, a database of membrane spanning protein segments. Biol Chem 347: 166.

    Google Scholar 

  • Hull R, 2001. Classifying reverse transcribing elements: a proposal and a challenge to the ICTV. Arch Virol 146: 2255–2261.

    Article  CAS  PubMed  Google Scholar 

  • Kim A, Terzian C, Santamaria P, Pelisson A, Purd’ Homme N, Bucheton A, 1994. Retroviruses in invertebrates: thegypsy retrotransposon is apparently an infectious retrovirus ofDrosophila melanogaster. Proc Natl Acad Sci USA 91: 1285–1289.

    Article  CAS  PubMed  Google Scholar 

  • Kim JK, Battini J-L, Manel N, Sitbon M, 2004. Emergence of vertebrate retroviruses and envelope capture. Virology 318: 183–191.

    Article  CAS  PubMed  Google Scholar 

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

    Article  CAS  PubMed  Google Scholar 

  • Kumar S, Tamura K, Nei M, 2004. MEGA3: Integrated software for Molecular Evolutionary Genetics Analysis and sequence alignment. Briefings in Bioinformatics 5: 150–163.

    Article  CAS  PubMed  Google Scholar 

  • Laten HM, Majumdar A, Gaucher EA, 1998. SIRE-1, a copia/Ty1-like retroelement from soybean, encodes a retroviral envelope-like protein. Proc Natl Acad Sci USA 95: 6897–6902.

    Article  CAS  PubMed  Google Scholar 

  • Laten HM, 1999. Phylogenetic evidence for Ty1-copia-like endogenous retroviruses in plant genomes. Genetica 107: 87–93.

    Article  CAS  PubMed  Google Scholar 

  • Laten HM, Havecker ER, Farmer LM, Voytas DF, 2003. SIRE-1, an endogenous family fromGlycine max, is highly homogenous and evolutionary young. Mol Biol Evol 20: 1–13.

    Article  Google Scholar 

  • Lerat E, Capy E, 1999. Retrotransposons and retroviruses: analysis of theenvelope gene. Mol Biol Evol 16: 1198–1207.

    CAS  PubMed  Google Scholar 

  • Malik HS, Henikoff S, Eickbush TH, 2000. Poised for contagion: evolutionary origins of the infectious abilities of invertebrate retroviruses. Genome Res 10: 1307–1318.

    Article  CAS  PubMed  Google Scholar 

  • Misseri Y, Labesse G, Bucheton A, Terzian C, 2003. Comparative sequence analysis and predications for theenvelope glycoproteins of insect retroviruses. Trends Microbiol 11: 253–256.

    Article  CAS  PubMed  Google Scholar 

  • Misseri Y, Cerutti M, Devauchelle G, Bucheton A, Terzian C, 2004. Analysis of theDrosophila gypsy endogenous retrovirusenvelope glycoprotein. J Gen. Virol 85: 3325–3331.

    Article  CAS  PubMed  Google Scholar 

  • Nei M, Gojobori T, 1986. Simple methods forestimating the numbers of synonymous and nonsynonymous nucleotidesubstitutions. Mol Biol Evol3: 418–426.

    Google Scholar 

  • Neumann P, Pozakova D, Koblizkova A, Macas J, 2005. Pigy, a new plant envelope-class LTR retrotransposon. Mol Gen Genomics 273: 43–53.

    Article  CAS  Google Scholar 

  • 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.

    Article  CAS  PubMed  Google Scholar 

  • Pereira V, 2004. Insertion bias and purifying selection of retrotransposons in theArabidopsis thaliana genome. Genome Biol 5: 79–89.

    Article  Google Scholar 

  • Peterson-Burch BD, Wright DA, Laten HM, Voytas DF 2000. Retroviruses in plants? TIG. 16: 151–152.

    Article  CAS  PubMed  Google Scholar 

  • Rost B, Casadio R, Farselli P, Sander C, 1995. Transmembrane helices predicted at 95% accuracy. Protein Sci 4: 521–533.

    Article  CAS  PubMed  Google Scholar 

  • Saitou N, Nei M, 1987. The neighbour-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4: 406–425.

    CAS  PubMed  Google Scholar 

  • Senchina DS, Alvarez I, Cronn RC, Liu B, Rong J, Noyes RD, et al. 2003. Rate variation among nuclear genes and the age of polyploidy inGossypium. Mol Biol Evol 20: 633–643.

    Article  CAS  PubMed  Google Scholar 

  • Song SU, Gerasimova M, Kurkulos M, Boeke JD, Corces VC, 1994. An env-like protein encoded by aDrosophila retroelement: evidence thatgypsy is an infectious retrovirus. Genes Dev 8: 2046–2057.

    Article  CAS  PubMed  Google Scholar 

  • Thompson JD, Higgins DG, Gibson TJ, 1994. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22: 4673–6480.

    Article  CAS  PubMed  Google Scholar 

  • Vanderwiel PS, Voytas DF, Wendel JF, 1993. Copia-like retrotransposable element evolution in diploid and polyploid cotton (Gossypium L.). J Mol Evol 36: 429–447.

    Article  CAS  PubMed  Google Scholar 

  • Vicient CM, Kalendar R, Schulman AH, 2001. Envelope-class retrovirus-like elements are widespread, transcribed and spliced, and insertionally polymorphic in plants. Genome Res 11: 2041–2049.

    Article  CAS  PubMed  Google Scholar 

  • Vitte C, Panaud Q, 2005. LTR retrotransposons and flowering plant genome size: emergence of the increase/decrease model. Cytogenet. Genome Res. 110: 91–107.

    Article  CAS  PubMed  Google Scholar 

  • Voytas DF, 1992.Arabidopsis and cotton (Gossypium) as models for studying copia-like retrotransposons evolution Genetica 86: 13–20.

    Article  Google Scholar 

  • Wendel JF, Cronn R, 2003. Polyploidy and the evolutionary history of cotton. Advances in Agronomy 78: 139–186.

    Article  Google Scholar 

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

    Article  CAS  PubMed  Google Scholar 

  • Wright DA, Voytas DF, 2001. Athila4 ofArabidopsis and Calypso of soybean define a lineage of endogenous plant retroviruses. Genome Res 12: 122–131.

    Article  Google Scholar 

  • Wright DA, Voytas DF, 1998. Potential retroviruses in plants: Tat1 is related to a group ofArabidopsis thaliana Ty3/gypsy retrotransposons that encode envelope-like proteins. Genetics 149: 703–715.

    CAS  PubMed  Google Scholar 

  • Yano ST, Panbehi B, Das A, Laten MH, 2005. Diaspora, a large family of Ty3-gypsy retrotransposons inGlycine max, is an envelope-less memberof endogenous plant retrovirus lineage. BMC Evol Biol 5: 30–44.

    Article  PubMed  Google Scholar 

  • Zaki EA, 2003. Plant retroviruses: structure, evolution and future applications. Afr J Biotech 2: 136–139.

    CAS  Google Scholar 

  • Zaki EA, Abdel Ghany A, 2004. Ty3/gypsy retro-transposons in Egyptian cotton (G. barbadense). J C Science 8: 179–185.

    CAS  Google Scholar 

  • Zaki EA, 2005. Ty1-copia group retrotransposon families in cultivated cottonsG. barbadense L. identified by reverse transcriptase domain analysis. DNA Seq 16: 288–294.

    CAS  PubMed  Google Scholar 

  • Zhang X, Wessler SR, 2004. Genome-widecomparative analysis of transposable elements in the related speciesArabidopsis thaliana andBrassica oleracea. Proc Natl Acad Sci USA 101: 5589–5594.

    Article  CAS  PubMed  Google Scholar 

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Authors and Affiliations

  1. Molecular plant pathology Department, Arid land research institute, Mubarak City for Research, Alexandria, Egypt

    E. E. Hafez

  2. Institute of Efficient Productivity, Zagazig University, El Zagazig, Egypt

    A. A. Abdel Ghany

  3. Plant Genome Mapping Laboratory, University of Georgia, Athens, Georgia, USA

    A. H. Paterson

  4. Nucleic Acids Research Department, Genetic Engineering and Biotechnology Research Institute (GEBRI), Mubarak City for Research, Alexandria, Egypt

    E. A. Zaki

  5. Division of Medical Genetics, The Saban Research Institute, Childrens Hospital Los Angeles, University of Southern California, 4650 Sunset Blvd, Mail Box 90, 90027, Los Angeles, CA, USA

    E. A. Zaki

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  1. E. E. Hafez
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  2. A. A. Abdel Ghany
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  3. A. H. Paterson
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  4. E. A. Zaki
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Correspondence to E. A. Zaki.

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Hafez, E.E., Abdel Ghany, A.A., Paterson, A.H. et al. Sequence heterogeneity of theenvelope-like domain in cultivated allotetraploidGossypium species and their diploid progenitors. J Appl Genet 50, 17–23 (2009). https://doi.org/10.1007/BF03195647

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  • DOI: https://doi.org/10.1007/BF03195647

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