Molecular Biology and Evolution, Vol 10, 1370-1379, Copyright © 1993 by Society for Molecular Biology and Evolution
MS Springer and RJ Britten
The gypsy group of long-terminal-repeat retrotransposons contains elements
having the same order of enzyme domains in the pol gene as do retroviruses.
Elements in the gypsy group are now known from yeast, filamentous fungi,
plants, insects, and echinoids. Reverse transcriptase and RNase H amino
acid sequences from elements in the gypsy group--including the recently
described SURL elements, TED, Cft1, and Ulysses,--were aligned and analyzed
by using parsimony and bootstrapping methods, with plant caulimoviruses
and/or retroviruses as outgroups. Clades supported at the 95% level after
bootstrapping include (1) 17.6 with 297 and (2) all of the SURL elements
together. Other likely relationships supported at lower bootstrap
confidence intervals include (1) SURL elements with mag, (2) 17.6 and 297
with TED, and this collective group with 412 and gypsy, (3) Tf1 with Cft1,
(4) IFG7 with Del, and (5) all of the retrotransposons in the gypsy group
together, to the exclusion of Ty3. In contrast with an earlier analysis,
our results place mag within the gypsy group rather than outside of a
cluster that contains gypsy group retrotransposons and plant
caulimoviruses. Several features of retrotransposon genomes provide further
support for some of the aforementioned relationships. The union of SURL
elements with mag is supported by the presence of two RNA binding sites in
the nucleocapsid protein. Location of the tRNA primer binding site and the
presence of a long open reading frame 3' to the pol gene support the
17.6-297-TED-412-gypsy cluster.
ORIGINAL ARTICLE
Phylogenetic relationships of reverse transcriptase and RNase H sequences and aspects of genome structure in the gypsy group of retrotransposons
Department of Biology, University of California.
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