• We are sorry, but NCBI web applications do not support your browser and may not function properly. More information
Logo of plntcellLink to Publisher's site
Plant Cell. Sep 1999; 11(9): 1769–1784.
PMCID: PMC144304

Retrotransposon BARE-1 and Its Role in Genome Evolution in the Genus Hordeum.


The replicative retrotransposon life cycle offers the potential for explosive increases in copy number and consequent inflation of genome size. The BARE-1 retrotransposon family of barley is conserved, disperse, and transcriptionally active. To assess the role of BARE-1 in genome evolution, we determined the copy number of its integrase, its reverse transcriptase, and its long terminal repeat (LTR) domains throughout the genus Hordeum. On average, BARE-1 contributes 13.7 x 10(3) full-length copies, amounting to 2.9% of the genome. The number increases with genome size. Two LTRs are associated with each internal domain in intact retrotransposons, but surprisingly, BARE-1 LTRs were considerably more prevalent than would be expected from the numbers of intact elements. The excess in LTRs increases as both genome size and BARE-1 genomic fraction decrease. Intrachromosomal homologous recombination between LTRs could explain the excess, removing BARE-1 elements and leaving behind solo LTRs, thereby reducing the complement of functional retrotransposons in the genome and providing at least a partial "return ticket from genomic obesity."

Full Text

The Full Text of this article is available as a PDF (535K).

Selected References

These references are in PubMed. This may not be the complete list of references from this article.
  • Adams SE, Mellor J, Gull K, Sim RB, Tuite MF, Kingsman SM, Kingsman AJ. The functions and relationships of Ty-VLP proteins in yeast reflect those of mammalian retroviral proteins. Cell. 1987 Apr 10;49(1):111–119. [PubMed]
  • Ahn S, Anderson JA, Sorrells ME, Tanksley SD. Homoeologous relationships of rice, wheat and maize chromosomes. Mol Gen Genet. 1993 Dec;241(5-6):483–490. [PubMed]
  • Athma P, Peterson T. Ac induces homologous recombination at the maize P locus. Genetics. 1991 May;128(1):163–173. [PMC free article] [PubMed]
  • Banville D, Rotaru M, Boie Y. The intracisternal A particle derived solo LTR promoter of the rat oncomodulin gene is not present in the mouse gene. Genetica. 1992;86(1-3):85–97. [PubMed]
  • Barakat A, Carels N, Bernardi G. The distribution of genes in the genomes of Gramineae. Proc Natl Acad Sci U S A. 1997 Jun 24;94(13):6857–6861. [PMC free article] [PubMed]
  • Bennetzen JL, Kellogg EA. Do Plants Have a One-Way Ticket to Genomic Obesity? Plant Cell. 1997 Sep;9(9):1509–1514. [PMC free article] [PubMed]
  • Bennetzen JL, Kellogg EA. Reply. Plant Cell. 1997 Nov;9(11):1901–1902. [PMC free article] [PubMed]
  • Bevan M, Bancroft I, Bent E, Love K, Goodman H, Dean C, Bergkamp R, Dirkse W, Van Staveren M, Stiekema W, et al. Analysis of 1.9 Mb of contiguous sequence from chromosome 4 of Arabidopsis thaliana. Nature. 1998 Jan 29;391(6666):485–488. [PubMed]
  • Blusch JH, Haltmeier M, Frech K, Sander I, Leib-Mösch C, Brack-Werner R, Werner T. Identification of endogenous retroviral sequences based on modular organization: proviral structure at the SSAV1 locus. Genomics. 1997 Jul 1;43(1):52–61. [PubMed]
  • Boeke JD, Chapman KB. Retrotransposition mechanisms. Curr Opin Cell Biol. 1991 Jun;3(3):502–507. [PubMed]
  • Tae Suk R o, Muramatsu M, Busch H. Labeling of RNA of isolated nucleoli with UTP-14C. Biochem Biophys Res Commun. 1964;14:149–155. [PubMed]
  • Chen M, SanMiguel P, de Oliveira AC, Woo SS, Zhang H, Wing RA, Bennetzen JL. Microcolinearity in sh2-homologous regions of the maize, rice, and sorghum genomes. Proc Natl Acad Sci U S A. 1997 Apr 1;94(7):3431–3435. [PMC free article] [PubMed]
  • Doolittle RF, Feng DF, Johnson MS, McClure MA. Origins and evolutionary relationships of retroviruses. Q Rev Biol. 1989 Mar;64(1):1–30. [PubMed]
  • Doolittle WF, Sapienza C. Selfish genes, the phenotype paradigm and genome evolution. Nature. 1980 Apr 17;284(5757):601–603. [PubMed]
  • 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 Jul 25;20(14):3639–3644. [PMC free article] [PubMed]
  • Gaut BS, Morton BR, McCaig BC, Clegg MT. Substitution rate comparisons between grasses and palms: synonymous rate differences at the nuclear gene Adh parallel rate differences at the plastid gene rbcL. Proc Natl Acad Sci U S A. 1996 Sep 17;93(19):10274–10279. [PMC free article] [PubMed]
  • Geyer PK, Green MM, Corces VG. Reversion of a gypsy-induced mutation at the yellow (y) locus of Drosophila melanogaster is associated with the insertion of a newly defined transposable element. Proc Natl Acad Sci U S A. 1988 Jun;85(11):3938–3942. [PMC free article] [PubMed]
  • Goodman HM, Ecker JR, Dean C. The genome of Arabidopsis thaliana. Proc Natl Acad Sci U S A. 1995 Nov 21;92(24):10831–10835. [PMC free article] [PubMed]
  • Grandbastien MA. Retroelements in higher plants. Trends Genet. 1992 Mar;8(3):103–108. [PubMed]
  • Gribbon BM, Pearce SR, Kalendar R, Schulman AH, Paulin L, Jack P, Kumar A, Flavell AJ. Phylogeny and transpositional activity of Ty1-copia group retrotransposons in cereal genomes. Mol Gen Genet. 1999 Jul;261(6):883–891. [PubMed]
  • Hirochika H. Activation of tobacco retrotransposons during tissue culture. EMBO J. 1993 Jun;12(6):2521–2528. [PMC free article] [PubMed]
  • Hirochika H, Fukuchi A, Kikuchi F. Retrotransposon families in rice. Mol Gen Genet. 1992 May;233(1-2):209–216. [PubMed]
  • Hsiao C, Chatterton NJ, Asay KH, Jensen KB. Phylogenetic relationships of the monogenomic species of the wheat tribe, Triticeae (Poaceae), inferred from nuclear rDNA (internal transcribed spacer) sequences. Genome. 1995 Apr;38(2):211–223. [PubMed]
  • Hu W, Timmermans MC, Messing J. Interchromosomal recombination in Zea mays. Genetics. 1998 Nov;150(3):1229–1237. [PMC free article] [PubMed]
  • Hueros G, Loarce Y, Ferrer E. A structural and evolutionary analysis of a dispersed repetitive sequence. Plant Mol Biol. 1993 Jul;22(4):635–643. [PubMed]
  • Hyman RW, Brunovskis I, Summers WC. DNA base sequence homology between coliphages T7 and phiII and between T3 and phiII as determined by heteroduplex mapping in the electron microscope. J Mol Biol. 1973 Jun 25;77(2):189–196. [PubMed]
  • Ikeda TM, Terachi T, Tsunewaki K. Variations in chloroplast proteins and nucleotide sequences of three chloroplast genes in Triticum and Aegilops. Jpn J Genet. 1992 Apr;67(2):111–123. [PubMed]
  • Kim JM, Vanguri S, Boeke JD, Gabriel A, Voytas DF. Transposable elements and genome organization: a comprehensive survey of retrotransposons revealed by the complete Saccharomyces cerevisiae genome sequence. Genome Res. 1998 May;8(5):464–478. [PubMed]
  • Kurata N, Umehara Y, Tanoue H, Sasaki T. Physical mapping of the rice genome with YAC clones. Plant Mol Biol. 1997 Sep;35(1-2):101–113. [PubMed]
  • Lucas H, Feuerbach F, Kunert K, Grandbastien MA, Caboche M. RNA-mediated transposition of the tobacco retrotransposon Tnt1 in Arabidopsis thaliana. EMBO J. 1995 May 15;14(10):2364–2373. [PMC free article] [PubMed]
  • Manninen I, Schulman AH. BARE-1, a copia-like retroelement in barley (Hordeum vulgare L.). Plant Mol Biol. 1993 Aug;22(5):829–846. [PubMed]
  • Matsuoka Y, Tsunewaki K. Wheat retrotransposon families identified by reverse transcriptase domain analysis. Mol Biol Evol. 1996 Dec;13(10):1384–1392. [PubMed]
  • Meinkoth J, Wahl G. Hybridization of nucleic acids immobilized on solid supports. Anal Biochem. 1984 May 1;138(2):267–284. [PubMed]
  • Nakamura Y, Gojobori T, Ikemura T. Codon usage tabulated from the international DNA sequence databases. Nucleic Acids Res. 1997 Jan 1;25(1):244–245. [PMC free article] [PubMed]
  • Noma K, Nakajima R, Ohtsubo H, Ohtsubo E. RIRE1, a retrotransposon from wild rice Oryza australiensis. Genes Genet Syst. 1997 Jun;72(3):131–140. [PubMed]
  • Ogihara Y, Terachi T, Sasakuma T. Molecular analysis of the hot spot region related to length mutations in wheat chloroplast DNAs. I. Nucleotide divergence of genes and intergenic spacer regions located in the hot spot region. Genetics. 1991 Nov;129(3):873–884. [PMC free article] [PubMed]
  • Orgel LE, Crick FH. Selfish DNA: the ultimate parasite. Nature. 1980 Apr 17;284(5757):604–607. [PubMed]
  • Panstruga R, Büschges R, Piffanelli P, Schulze-Lefert P. A contiguous 60 kb genomic stretch from barley reveals molecular evidence for gene islands in a monocot genome. Nucleic Acids Res. 1998 Feb 15;26(4):1056–1062. [PMC free article] [PubMed]
  • Parket A, Inbar O, Kupiec M. Recombination of Ty elements in yeast can be induced by a double-strand break. Genetics. 1995 May;140(1):67–77. [PMC free article] [PubMed]
  • Pearce SR, Harrison G, Li D, Heslop-Harrison J, Kumar A, Flavell AJ. The Ty1-copia group retrotransposons in Vicia species: copy number, sequence heterogeneity and chromosomal localisation. Mol Gen Genet. 1996 Feb 25;250(3):305–315. [PubMed]
  • Pearce SR, Pich U, Harrison G, Flavell AJ, Heslop-Harrison JS, Schubert I, Kumar A. The Ty1-copia group retrotransposons of Allium cepa are distributed throughout the chromosomes but are enriched in the terminal heterochromatin. Chromosome Res. 1996 Aug;4(5):357–364. [PubMed]
  • Petrov D. Slow but Steady: Reduction of Genome Size through Biased Mutation. Plant Cell. 1997 Nov;9(11):1900–1901. [PMC free article] [PubMed]
  • Puchta H, Kocher S, Hohn B. Extrachromosomal homologous DNA recombination in plant cells is fast and is not affected by CpG methylation. Mol Cell Biol. 1992 Aug;12(8):3372–3379. [PMC free article] [PubMed]
  • Ramsay L, Macaulay M, Cardle L, Morgante M, degli Ivanissevich S, Maestri E, Powell W, Waugh R. Intimate association of microsatellite repeats with retrotransposons and other dispersed repetitive elements in barley. Plant J. 1999 Feb;17(4):415–425. [PubMed]
  • Royo J, Nass N, Matton DP, Okamoto S, Clarke AE, Newbigin E. A retrotransposon-like sequence linked to the S-locus of Nicotiana alata is expressed in styles in response to touch. Mol Gen Genet. 1996 Feb 5;250(2):180–188. [PubMed]
  • Saghai Maroof MA, Allard RW, Zhang QF. Genetic diversity and ecogeographical differentiation among ribosomal DNA alleles in wild and cultivated barley. Proc Natl Acad Sci U S A. 1990 Nov;87(21):8486–8490. [PMC free article] [PubMed]
  • SanMiguel P, Tikhonov A, Jin YK, Motchoulskaia N, Zakharov D, Melake-Berhan A, Springer PS, Edwards KJ, Lee M, Avramova Z, et al. Nested retrotransposons in the intergenic regions of the maize genome. Science. 1996 Nov 1;274(5288):765–768. [PubMed]
  • SanMiguel P, Gaut BS, Tikhonov A, Nakajima Y, Bennetzen JL. The paleontology of intergene retrotransposons of maize. Nat Genet. 1998 Sep;20(1):43–45. [PubMed]
  • Schwarzacher T, Leitch AR. Enzymatic treatment of plant material to spread chromosomes for in situ hybridization. Methods Mol Biol. 1994;28:153–160. [PubMed]
  • Sentry JW, Smyth DR. An element with long terminal repeats and its variant arrangements in the genome of Lilium henryi. Mol Gen Genet. 1989 Jan;215(2):349–354. [PubMed]
  • Suoniemi A, Anamthawat-Jónsson K, Arna T, Schulman AH. Retrotransposon BARE-1 is a major, dispersed component of the barley (Hordeum vulgare L.) genome. Plant Mol Biol. 1996 Mar;30(6):1321–1329. [PubMed]
  • 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 May;31(2):295–306. [PubMed]
  • Suoniemi A, Schmidt D, Schulman AH. BARE-1 insertion site preferences and evolutionary conservation of RNA and cDNA processing sites. Genetica. 1997;100(1-3):219–230. [PubMed]
  • Suoniemi A, Tanskanen J, Pentikäinen O, Johnson MS, Schulman AH. The core domain of retrotransposon integrase in Hordeum: predicted structure and evolution. Mol Biol Evol. 1998 Sep;15(9):1135–1144. [PubMed]
  • Suoniemi A, Tanskanen J, Schulman AH. Gypsy-like retrotransposons are widespread in the plant kingdom. Plant J. 1998 Mar;13(5):699–705. [PubMed]
  • Takeda S, Sugimoto K, Otsuki H, Hirochika H. Transcriptional activation of the tobacco retrotransposon Tto1 by wounding and methyl jasmonate. Plant Mol Biol. 1998 Feb;36(3):365–376. [PubMed]
  • Thomas CA., Jr The genetic organization of chromosomes. Annu Rev Genet. 1971;5:237–256. [PubMed]
  • Waugh R, McLean K, Flavell AJ, Pearce SR, Kumar A, Thomas BB, Powell W. Genetic distribution of Bare-1-like retrotransposable elements in the barley genome revealed by sequence-specific amplification polymorphisms (S-SAP). Mol Gen Genet. 1997 Feb 27;253(6):687–694. [PubMed]
  • Vernhettes S, Grandbastien MA, Casacuberta JM. In vivo characterization of transcriptional regulatory sequences involved in the defence-associated expression of the tobacco retrotransposon Tnt1. Plant Mol Biol. 1997 Nov;35(5):673–679. [PubMed]
  • Vershinin AV, Salina EA, Solovyov VV, Timofeyeva LL. Genomic organization, evolution, and structural peculiarities of highly repetitive DNA of Hordeum vulgare. Genome. 1990 Jun;33(3):441–449. [PubMed]
  • Voytas DF, Naylor GJ. Rapid flux in plant genomes. Nat Genet. 1998 Sep;20(1):6–7. [PubMed]
  • Voytas DF, Cummings MP, Koniczny A, Ausubel FM, Rodermel SR. copia-like retrotransposons are ubiquitous among plants. Proc Natl Acad Sci U S A. 1992 Aug 1;89(15):7124–7128. [PMC free article] [PubMed]
  • Wessler SR. Turned on by stress. Plant retrotransposons. Curr Biol. 1996 Aug 1;6(8):959–961. [PubMed]
  • Wessler SR, Bureau TE, White SE. LTR-retrotransposons and MITEs: important players in the evolution of plant genomes. Curr Opin Genet Dev. 1995 Dec;5(6):814–821. [PubMed]
  • Zhou J, Kilian A, Warner RL, Kleinhofs A. Variation of nitrate reductase genes in selected grass species. Genome. 1995 Oct;38(5):919–927. [PubMed]

Articles from The Plant Cell are provided here courtesy of American Society of Plant Biologists


Related citations in PubMed

See reviews...See all...

Cited by other articles in PMC

See all...


Recent Activity

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

See more...