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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C. E. Perez-Gonzalez and T. H. Eickbush Rates of R1 and R2 Retrotransposition and Elimination From the rDNA Locus of Drosophila melanogaster Genetics, October 1, 2002; 162(2): 799 - 811. [Abstract] [Full Text] [PDF]
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A. Bibillo and T. H. Eickbush High Processivity of the Reverse Transcriptase from a Non-long Terminal Repeat Retrotransposon J. Biol. Chem., September 13, 2002; 277(38): 34836 - 34845. [Abstract] [Full Text] [PDF]
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I. Ovchinnikov, A. Rubin, and G. D. Swergold Tracing the LINEs of human evolution PNAS, August 6, 2002; 99(16): 10522 - 10527. [Abstract] [Full Text] [PDF]
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M. Olivares, J. L. Garcia-Perez, M. C. Thomas, S. R. Heras, and M. C. Lopez The Non-LTR (Long Terminal Repeat) Retrotransposon L1Tc from Trypanosoma cruzi Codes for a Protein with RNase H Activity J. Biol. Chem., July 26, 2002; 277(31): 28025 - 28030. [Abstract] [Full Text] [PDF]
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E. Casacuberta and M.-L. Pardue Coevolution of the Telomeric Retrotransposons Across Drosophila Species Genetics, July 1, 2002; 161(3): 1113 - 1124. [Abstract] [Full Text] [PDF]
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C. Neuveglise, H. Feldmann, E. Bon, C. Gaillardin, and a. S. Casaregola Genomic Evolution of the Long Terminal Repeat Retrotransposons in Hemiascomycetous Yeasts Genome Res., June 1, 2002; 12(6): 930 - 943. [Abstract] [Full Text] [PDF]
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M. Plohl, E. Prats, A. Martinez-Lage, A. Gonzalez-Tizon, J. Mendez, and L. Cornudella Telomeric Localization of the Vertebrate-type Hexamer Repeat, (TTAGGG)n, in the Wedgeshell Clam Donax trunculus and Other Marine Invertebrate Genomes J. Biol. Chem., May 24, 2002; 277(22): 19839 - 19846. [Abstract] [Full Text] [PDF]
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W. D. Burke, H. S. Malik, S. M. Rich, and T. H. Eickbush Ancient Lineages of Non-LTR Retrotransposons in the Primitive Eukaryote, Giardia lamblia Mol. Biol. Evol., May 1, 2002; 19(5): 619 - 630. [Abstract] [Full Text] [PDF]
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S. Casaregola, C. Neuveglise, E. Bon, and C. Gaillardin Ylli, a Non-LTR Retrotransposon L1 Family in the Dimorphic Yeast Yarrowia lipolytica Mol. Biol. Evol., May 1, 2002; 19(5): 664 - 677. [Abstract] [Full Text] [PDF]
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S. Rashkova, S. E. Karam, and M.-L. Pardue Element-specific localization of Drosophila retrotransposon Gag proteins occurs in both nucleus and cytoplasm PNAS, March 19, 2002; 99(6): 3621 - 3626. [Abstract] [Full Text] [PDF]
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I. Ogiwara, M. Miya, K. Ohshima, and N. Okada V-SINEs: A New Superfamily of Vertebrate SINEs That Are Widespread in Vertebrate Genomes and Retain a Strongly Conserved Segment within Each Repetitive Unit Genome Res., February 1, 2002; 12(2): 316 - 324. [Abstract] [Full Text] [PDF]
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 A. Bird DNA methylation patterns and epigenetic memory Genes & Dev., January 1, 2002; 16(1): 6 - 21. [Full Text] [PDF]
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I. R. Arkhipova and H. G. Morrison From the Cover: Three retrotransposon families in the genome of Giardia lamblia: Two telomeric, one dead PNAS, December 4, 2001; 98(25): 14497 - 14502. [Abstract] [Full Text] [PDF]
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E. M. Ostertag and H. H. Kazazian Jr. Twin Priming: A Proposed Mechanism for the Creation of Inversions in L1 Retrotransposition Genome Res., December 1, 2001; 11(12): 2059 - 2065. [Abstract] [Full Text] [PDF]
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S. Boissinot and A. V. Furano Adaptive Evolution in LINE-1 Retrotransposons Mol. Biol. Evol., December 1, 2001; 18(12): 2186 - 2194. [Abstract] [Full Text] [PDF]
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N. Lovsin, F. Gubensek, and D. Kordi Evolutionary Dynamics in a Novel L2 Clade of Non-LTR Retrotransposons in Deuterostomia Mol. Biol. Evol., December 1, 2001; 18(12): 2213 - 2224. [Abstract] [Full Text] [PDF]
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A. Lenoir, L. Lavie, J.-L. Prieto, C. Goubely, J.-C. Cote, T. Pelissier, and J.-M. Deragon The Evolutionary Origin and Genomic Organization of SINEs in Arabidopsis thaliana Mol. Biol. Evol., December 1, 2001; 18(12): 2315 - 2322. [Abstract] [Full Text] [PDF]
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V. Zupunski, F. Gubensek, and D. Kordi Evolutionary Dynamics and Evolutionary History in the RTE Clade of Non-LTR Retrotransposons Mol. Biol. Evol., October 1, 2001; 18(10): 1849 - 1863. [Abstract] [Full Text] [PDF]
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