Skip to main content
NCBI home page
Proceedings of the National Academy of Sciences of the United States of America logoLink to Proceedings of the National Academy of Sciences of the United States of America
. 1992 Aug 1;89(15):7124–7128. doi: 10.1073/pnas.89.15.7124

copia-like retrotransposons are ubiquitous among plants.

D F Voytas 1, M P Cummings 1, A Koniczny 1, F M Ausubel 1, S R Rodermel 1
PMCID: PMC49658  PMID: 1379734

Abstract

Transposable genetic elements are assumed to be a feature of all eukaryotic genomes. Their identification, however, has largely been haphazard, limited principally to organisms subjected to molecular or genetic scrutiny. We assessed the phylogenetic distribution of copia-like retrotransposons, a class of transposable element that proliferates by reverse transcription, using a polymerase chain reaction assay designed to detect copia-like element reverse transcriptase sequences. copia-like retrotransposons were identified in 64 plant species as well as the photosynthetic protist Volvox carteri. The plant species included representatives from 9 of 10 plant divisions, including bryophytes, lycopods, ferns, gymnosperms, and angiosperms. DNA sequence analysis of 29 cloned PCR products and of a maize retrotransposon cDNA confirmed the identity of these sequences as copia-like reverse transcriptase sequences, thereby demonstrating that this class of retrotransposons is a ubiquitous component of plant genomes.

Full text

PDF
7124

Images in this article

7125Image
on p.7125
7126Image
on p.7126

Selected References

These references are in PubMed. This may not be the complete list of references from this article.

  1. Atchley W. R., Fitch W. M. Gene trees and the origins of inbred strains of mice. Science. 1991 Oct 25;254(5031):554–558. doi: 10.1126/science.1948030. [DOI] [PubMed] [Google Scholar]
  2. Boeke J. D., Eichinger D., Castrillon D., Fink G. R. The Saccharomyces cerevisiae genome contains functional and nonfunctional copies of transposon Ty1. Mol Cell Biol. 1988 Apr;8(4):1432–1442. doi: 10.1128/mcb.8.4.1432. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Boeke J. D., Garfinkel D. J., Styles C. A., Fink G. R. Ty elements transpose through an RNA intermediate. Cell. 1985 Mar;40(3):491–500. doi: 10.1016/0092-8674(85)90197-7. [DOI] [PubMed] [Google Scholar]
  4. Camirand A., Brisson N. The complete nucleotide sequence of the Tst1 retrotransposon of potato. Nucleic Acids Res. 1990 Aug 25;18(16):4929–4929. doi: 10.1093/nar/18.16.4929. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Church G. M., Gilbert W. Genomic sequencing. Proc Natl Acad Sci U S A. 1984 Apr;81(7):1991–1995. doi: 10.1073/pnas.81.7.1991. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Devereux J., Haeberli P., Smithies O. A comprehensive set of sequence analysis programs for the VAX. Nucleic Acids Res. 1984 Jan 11;12(1 Pt 1):387–395. doi: 10.1093/nar/12.1part1.387. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Dombroski B. A., Mathias S. L., Nanthakumar E., Scott A. F., Kazazian H. H., Jr Isolation of an active human transposable element. Science. 1991 Dec 20;254(5039):1805–1808. doi: 10.1126/science.1662412. [DOI] [PubMed] [Google Scholar]
  8. Doolittle R. F., Feng D. F., Johnson M. S., McClure M. A. Origins and evolutionary relationships of retroviruses. Q Rev Biol. 1989 Mar;64(1):1–30. doi: 10.1086/416128. [DOI] [PubMed] [Google Scholar]
  9. Flavell A. J., Smith D. B., Kumar A. Extreme heterogeneity of Ty1-copia group retrotransposons in plants. Mol Gen Genet. 1992 Jan;231(2):233–242. doi: 10.1007/BF00279796. [DOI] [PubMed] [Google Scholar]
  10. Fourcade-Peronnet F., d'Auriol L., Becker J., Galibert F., Best-Belpomme M. Primary structure and functional organization of Drosophila 1731 retrotransposon. Nucleic Acids Res. 1988 Jul 11;16(13):6113–6125. doi: 10.1093/nar/16.13.6113. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Grandbastien M. A., 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. doi: 10.1038/337376a0. [DOI] [PubMed] [Google Scholar]
  12. Hein J. A new method that simultaneously aligns and reconstructs ancestral sequences for any number of homologous sequences, when the phylogeny is given. Mol Biol Evol. 1989 Nov;6(6):649–668. doi: 10.1093/oxfordjournals.molbev.a040577. [DOI] [PubMed] [Google Scholar]
  13. Hein J. A tree reconstruction method that is economical in the number of pairwise comparisons used. Mol Biol Evol. 1989 Nov;6(6):669–684. doi: 10.1093/oxfordjournals.molbev.a040578. [DOI] [PubMed] [Google Scholar]
  14. Higgins D. G., Sharp P. M. Fast and sensitive multiple sequence alignments on a microcomputer. Comput Appl Biosci. 1989 Apr;5(2):151–153. doi: 10.1093/bioinformatics/5.2.151. [DOI] [PubMed] [Google Scholar]
  15. Holland J., Spindler K., Horodyski F., Grabau E., Nichol S., VandePol S. Rapid evolution of RNA genomes. Science. 1982 Mar 26;215(4540):1577–1585. doi: 10.1126/science.7041255. [DOI] [PubMed] [Google Scholar]
  16. Hu W. S., Temin H. M. Retroviral recombination and reverse transcription. Science. 1990 Nov 30;250(4985):1227–1233. doi: 10.1126/science.1700865. [DOI] [PubMed] [Google Scholar]
  17. Konieczny A., Voytas D. F., Cummings M. P., Ausubel F. M. A superfamily of Arabidopsis thaliana retrotransposons. Genetics. 1991 Apr;127(4):801–809. doi: 10.1093/genetics/127.4.801. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Moore G., Lucas H., Batty N., Flavell R. A family of retrotransposons and associated genomic variation in wheat. Genomics. 1991 Jun;10(2):461–468. doi: 10.1016/0888-7543(91)90333-a. [DOI] [PubMed] [Google Scholar]
  19. Mount S. M., Rubin G. M. Complete nucleotide sequence of the Drosophila transposable element copia: homology between copia and retroviral proteins. Mol Cell Biol. 1985 Jul;5(7):1630–1638. doi: 10.1128/mcb.5.7.1630. [DOI] [PMC free article] [PubMed] [Google Scholar]
  20. Rothnie H. M., McCurrach K. J., Glover L. A., Hardman N. Retrotransposon-like nature of Tp1 elements: implications for the organisation of highly repetitive, hypermethylated DNA in the genome of Physarum polycephalum. Nucleic Acids Res. 1991 Jan 25;19(2):279–286. doi: 10.1093/nar/19.2.279. [DOI] [PMC free article] [PubMed] [Google Scholar]
  21. Sarkar G., Sommer S. S. Shedding light on PCR contamination. Nature. 1990 Jan 4;343(6253):27–27. doi: 10.1038/343027a0. [DOI] [PubMed] [Google Scholar]
  22. Voytas D. F., Ausubel F. M. A copia-like transposable element family in Arabidopsis thaliana. Nature. 1988 Nov 17;336(6196):242–244. doi: 10.1038/336242a0. [DOI] [PubMed] [Google Scholar]
  23. Voytas D. F., Konieczny A., Cummings M. P., Ausubel F. M. The structure, distribution and evolution of the Ta1 retrotransposable element family of Arabidopsis thaliana. Genetics. 1990 Nov;126(3):713–721. doi: 10.1093/genetics/126.3.713. [DOI] [PMC free article] [PubMed] [Google Scholar]
  24. Xiong Y., Eickbush T. H. Origin and evolution of retroelements based upon their reverse transcriptase sequences. EMBO J. 1990 Oct;9(10):3353–3362. doi: 10.1002/j.1460-2075.1990.tb07536.x. [DOI] [PMC free article] [PubMed] [Google Scholar]

Articles from Proceedings of the National Academy of Sciences of the United States of America are provided here courtesy of National Academy of Sciences

RESOURCES