Plant Molecular Biology 38: 461–465, 1998.
© 1998 Kluwer Academic Publishers. Printed in the Netherlands.
Retrotransposon-like sequences integrated into the genome of pineapple,
, John E. Thomas
and Ralf G. Dietzgen
Queensland Department of Primary Industries, Queensland Agricultural Biotechnology Centre, The University
of Queensland, St Lucia, Brisbane, Queensland, 4072, Australia (
author for correspondence);
Department of Primary Industries, Plant Protection Unit, Meiers Road, Indooroopilly, Brisbane, Queensland,
Received 17 April 1997; accepted in revised form 8 April 1998
Key words: Ananas, del1, integrase, pineapple, retrotransposon, Ty3/gypsy
Retrotransposon-like sequences have been serendipitously detected in the genome of commercial pineapple,
Ananas comosus. The sequence from a 2.6 kb cloned fragment of this element had greatest similarity to the del1
Lilium henryi retrotransposon and the gypsy/Ty3 group of retroelements. The order of the genes from 5
reverse transcriptase, ribonuclease H and integrase. The integrase domain contained the amino acid sequence motifs
which have been associated with recognition of the long terminal repeats and with the cutting/joining reactions
required for integration of similar retroelements into the host genome. The retrotransposon existed as a population
of variable sequences which were dispersed throughout the genome of pineapple. Southern hybridisation showed
that the retrotransposon had integrated repeatedly into the pineapple genome. The reading frame of the element
was not interrupted by stop codons, suggesting that it is still potentially capable of transposing. This is the ﬁrst
report of a retrotransposon in pineapple, which we have called dea1 (for dispersed element of Ananas).
Retrotransposons are non-infectious DNA elements
which can transpose via an RNA intermediate 
and are ubiquitous in eukaryotes . The class
of retrotransposons which contain long terminal re-
peats (LTR) is composed of the Ty1/copia and the
Ty3/gypsy group elements, named after representative
retrotransposon families from Saccharomyces cere-
visiae and Drosophila melanogaster, respectively .
The Ty3/gypsy elements are related to retroviruses and
plant pararetroviruses on the basis of reverse tran-
scriptase sequence homologies and have enzymatic
domains in the order from 5
of aspartic protease,
reverse transcriptase (RT), ribonuclease H (RNase H)
and integrase . The Ty3/gypsy elements del1 and
IFG7 were both identiﬁed by their high copy number
(>10000) in the large genomes of lilies and pine trees.
The nucleotide sequence data reported will appear in the
EMBL and GenBank Nucleotide Sequence Databases under the
accession number Y12432.
Another Ty3/gypsy element, Tna1, with homology to
del1 from Lilium henryi [11, 12] was discovered while
characterising the gene required for self incompatibil-
ity in Nicotiana alata . Several Ty3/gypsy elements
were recently described in the intergenic regions of the
maize genome . In this report we describe the ﬁrst
retrotransposon from A. comosus.
Discovery and sequence variability of the pineapple
While trying to obtain additional sequence informa-
tion from the dsDNA genome of the plant pararetro-
virus pineapple bacilliform badnavirus (PBV) ,
single-primer polymerase chain reaction (PCR) -
ampliﬁed fragments of pineapple DNA were cloned
which had similarity to the RT, RNase H and in-
tegrase genes of retrotransposons. Primers designed
from these cloned sequences and a mixture of Taq
and Pwo DNA polymerases allowed ampliﬁcation