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Proc Natl Acad Sci U S A. Apr 2, 1996; 93(7): 2708–2713.
PMCID: PMC39695

The genomic and physical organization of Ty1-copia-like sequences as a component of large genomes in Pinus elliottii var. elliottii and other gymnosperms.

Abstract

A DNA sequence, TPE1, representing the internal domain of a Ty1-copia retroelement, was isolated from genomic DNA of Pinus elliottii Engelm. var. elliottii (slash pine). Genomic Southern analysis showed that this sequence, carrying partial reverse transcriptase and integrase gene sequences, is highly amplified within the genome of slash pine and part of a dispersed element >4.8 kbp. Fluorescent in situ hybridization to metaphase chromosomes shows that the element is relatively uniformly dispersed over all 12 chromosome pairs and is highly abundant in the genome. It is largely excluded from centromeric regions and intercalary chromosomal sites representing the 18S-5.8S-25S rRNA genes. Southern hybridization with specific DNA probes for the reverse transcriptase gene shows that TPE1 represents a large subgroup of heterogeneous Ty1-copia retrotransposons in Pinus species. Because no TPE1 transcription could be detected, it is most likely an inactive element--at least in needle tissue. Further evidence for inactivity was found in recombinant reverse transcriptase and integrase sequences. The distribution of TPE1 within different gymnosperms that contain Ty1-copia group retrotransposons, as shown by a PCR assay, was investigated by Southern hybridization. The TPE1 family is highly amplified and conserved in all Pinus species analyzed, showing a similar genomic organization in the three- and five-needle pine species investigated. It is also present in spruce, bald cypress (swamp cypress), and in gingko but in fewer copies and a different genomic organization.

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Selected References

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  • 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]
  • Voytas DF, Ausubel FM. A copia-like transposable element family in Arabidopsis thaliana. Nature. 1988 Nov 17;336(6196):242–244. [PubMed]
  • Grandbastien MA, Spielmann A, Caboche M. Tnt1, a mobile retroviral-like transposable element of tobacco isolated by plant cell genetics. Nature. 1989 Jan 26;337(6205):376–380. [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]
  • Hirochika H, Hirochika R. Ty1-copia group retrotransposons as ubiquitous components of plant genomes. Jpn J Genet. 1993 Feb;68(1):35–46. [PubMed]
  • Camirand A, Brisson N. The complete nucleotide sequence of the Tst1 retrotransposon of potato. Nucleic Acids Res. 1990 Aug 25;18(16):4929–4929. [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]
  • White SE, Habera LF, Wessler SR. Retrotransposons in the flanking regions of normal plant genes: a role for copia-like elements in the evolution of gene structure and expression. Proc Natl Acad Sci U S A. 1994 Dec 6;91(25):11792–11796. [PMC free article] [PubMed]
  • Flavell AJ. Ty1-copia group retrotransposons and the evolution of retroelements in the eukaryotes. Genetica. 1992;86(1-3):203–214. [PubMed]
  • Mount SM, Rubin GM. Complete nucleotide sequence of the Drosophila transposable element copia: homology between copia and retroviral proteins. Mol Cell Biol. 1985 Jul;5(7):1630–1638. [PMC free article] [PubMed]
  • Xiong Y, Eickbush TH. Origin and evolution of retroelements based upon their reverse transcriptase sequences. EMBO J. 1990 Oct;9(10):3353–3362. [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]
  • Tulsieram LK, Glaubitz JC, Kiss G, Carlson JE. Single tree genetic linkage mapping in conifers using haploid DNA from megagametophytes. Biotechnology (N Y) 1992 Jun;10(6):686–690. [PubMed]
  • Knapp DW, Richardson RC, Chan TC, Bottoms GD, Widmer WR, DeNicola DB, Teclaw R, Bonney PL, Kuczek T. Piroxicam therapy in 34 dogs with transitional cell carcinoma of the urinary bladder. J Vet Intern Med. 1994 Jul-Aug;8(4):273–278. [PubMed]
  • Wagner DB, Furnier GR, Saghai-Maroof MA, Williams SM, Dancik BP, Allard RW. Chloroplast DNA polymorphisms in lodgepole and jack pines and their hybrids. Proc Natl Acad Sci U S A. 1987 Apr;84(7):2097–2100. [PMC free article] [PubMed]
  • Vieira J, Messing J. The pUC plasmids, an M13mp7-derived system for insertion mutagenesis and sequencing with synthetic universal primers. Gene. 1982 Oct;19(3):259–268. [PubMed]
  • Gerlach WL, Bedbrook JR. Cloning and characterization of ribosomal RNA genes from wheat and barley. Nucleic Acids Res. 1979 Dec 11;7(7):1869–1885. [PMC free article] [PubMed]
  • Flavell AJ, Smith DB, Kumar A. Extreme heterogeneity of Ty1-copia group retrotransposons in plants. Mol Gen Genet. 1992 Jan;231(2):233–242. [PubMed]
  • Pouteau S, Huttner E, Grandbastien MA, Caboche M. Specific expression of the tobacco Tnt1 retrotransposon in protoplasts. EMBO J. 1991 Jul;10(7):1911–1918. [PMC free article] [PubMed]
  • Konieczny A, Voytas DF, Cummings MP, Ausubel FM. A superfamily of Arabidopsis thaliana retrotransposons. Genetics. 1991 Apr;127(4):801–809. [PMC free article] [PubMed]
  • Moore G, Cheung W, Schwarzacher T, Flavell R. BIS 1, a major component of the cereal genome and a tool for studying genomic organization. Genomics. 1991 Jun;10(2):469–476. [PubMed]
  • Schmidt T, Kubis S, Heslop-Harrison JS. Analysis and chromosomal localization of retrotransposons in sugar beet (Beta vulgaris L.): LINEs and Ty1-copia-like elements as major components of the genome. Chromosome Res. 1995 Sep;3(6):335–345. [PubMed]
  • Hirochika H, Fukuchi A, Kikuchi F. Retrotransposon families in rice. Mol Gen Genet. 1992 May;233(1-2):209–216. [PubMed]
  • VanderWiel PL, Voytas DF, Wendel JF. Copia-like retrotransposable element evolution in diploid and polyploid cotton (Gossypium L.). J Mol Evol. 1993 May;36(5):429–447. [PubMed]

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