Molecular Biology and Evolution, Vol 16, 793-805, Copyright © 1999 by Society for Molecular Biology and Evolution
HS Malik, WD Burke and TH Eickbush
A comprehensive phylogenetic analysis was conducted of non-long-
terminal-repeat (non-LTR) retrotransposons based on an extended sequence
alignment of their reverse transcriptase (RT) domain. The 440 amino acid
positions used included a region proposed to be similar to the "thumb" of
the right-handed RT structure found in retroviruses. All identified non-LTR
elements could be grouped into 11 distinct clades. Using the rates of
sequence change derived from studies of the vertical inheritance of R1 and
R2 elements in arthropods as a comparison, we found no evidence for the
horizontal transmission of non-LTR elements. Assuming vertical descent, the
phylogeny suggested that non-LTR elements are as old as eukaryotes, with
each of the 11 clades dating back to the Precambrian era. The analysis
enabled us to propose a simple chronology for the acquisition of different
enzymatic domains in the evolution of the non-LTR class of
retrotransposons. The first non- LTR elements were sequence specific by
virtue of a restriction-enzyme- like endonuclease located downstream of the
RT domain. Evolving from this original group were elements (eight clades)
that acquired an apurinic-apyrimidic endonuclease-like domain upstream of
the RT domain. Finally, four of these clades have inherited an RNase H
domain downstream of the RT domain. The phylogenies of the AP endonuclease
and RNase H domains were also determined for this report and are consistent
with the monophyletic acquisition of these domains. These studies represent
the most comprehensive effort to date to trace the evolution of a major
class of transposable elements.
ORIGINAL ARTICLE
The age and evolution of non-LTR retrotransposable elements
Department of Biology, University of Rochester, New York 14627, USA.
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