Highly heterogeneous families of Ty1/copia retrotransposons in the Lycopersicon chilense genome

Gene. 1998 Nov 19;222(2):223-8. doi: 10.1016/s0378-1119(98)00486-7.

Abstract

We have used the degenerated oligonucleotide primers-PCR (DOP-PCR) technique to determine the presence of Ty1/copia-related retrotransposons in the wild species of tomato, Lycopersicon chilense. Using degenerated oligonucleotides corresponding to highly conserved domains in the Ty1/copia retrotransposons, fragments of roughly 300 bp were obtained by PCR amplification. These were cloned in a plasmid vector and the nucleotide sequence determined for 20 clones, 19 of which showed sequence homology to retrotransposon-related sequences. Comparison of the deduced amino-acid sequence of these clones with those reported for other retrotransposons has allowed their classification into four distinct families: TLC1-TLC4. The level of amino-acid sequence similarity between these elements extends from 66.7% (between TLC1 and TLC2) to 42.6% (between TLC2 and TLC3). Altogether, the four families comprise about 0.17% of the L. chilense genome. RT-PCR analysis shows that the four TLC families are transcriptionally active, suggesting a mechanism for the generation of the observed diversity between the L. chilense retrotransposons.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Sequence
  • Base Sequence
  • DNA Primers / genetics
  • DNA, Plant / genetics
  • Evolution, Molecular
  • Genome, Plant*
  • Lycopersicon esculentum / genetics*
  • Molecular Sequence Data
  • Plant Proteins / genetics
  • Polymerase Chain Reaction
  • Retroelements*
  • Sequence Homology, Amino Acid

Substances

  • DNA Primers
  • DNA, Plant
  • Plant Proteins
  • Retroelements

Associated data

  • GENBANK/AJ001211
  • GENBANK/AJ001212
  • GENBANK/AJ001213
  • GENBANK/AJ001214