MBE Advance Access originally published online on July 13, 2005
Molecular Biology and Evolution 2005 22(11):2157-2165; doi:10.1093/molbev/msi210
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Research Article |
Long-Term Inheritance of the 28S rDNA-Specific Retrotransposon R2
Department of Integrated Biosciences, Graduate School of Frontier Sciences, University of Tokyo, Chiba, Japan
E-mail: haruh{at}k.u-tokyo.ac.jp.
R2 is a non–long-terminal-repeat (LTR) retrotransposon that inserts specifically into 28S rDNA. R2 has been identified in many species of arthropods and three species of chordates. R2 may be even more widely distributed in animals, and its origin may be traceable to early animal evolution. In this study, we identified R2 elements in medaka fish, White Cloud Mountain minnow, Reeves' turtle, hagfish, sea lilies, and some arthropod species, using degenerate polymerase chain reaction methods. We also identified two R2 elements from the public genomic sequence database of the bloodfluke Schistosoma mansoni. One of the two bloodfluke R2 elements has two zinc-finger motifs at the N-terminus; this differs from other known R2 elements, which have one or three zinc-finger motifs. Phylogenetic analysis revealed that the whole phylogeny of R2 can be divided into 11 parts (subclades), in which the local R2 phylogeny and the corresponding host phylogeny are consistent. Divergence-versus-age analysis revealed that there is no reliable evidence for the horizontal transfer of R2 but supports the proposition that R2 has been vertically transferred since before the divergence of the deuterostomes and protostomes. The seeming inconsistency between the R2 phylogeny and the phylogeny of their hosts is due to the existence of paralogous lineages. The number of N-terminal zinc-finger motifs is consistent with the deep phylogeny of R2 and indicates that the common ancestor of R2 had three zinc-finger motifs at the N-terminus. This study revealed the long-term vertical inheritance and the ancient origin of sequence specificity of R2, both of which seem applicable to some other non-LTR retrotransposons.
Key Words: non-LTR retrotransposons • R2 • sequence specificity • evolution • ribosomal RNA • vertical transmission
CiteULike 
Connotea 
Del.icio.us What's this?
This article has been cited by other articles:
|
|
 |
|
  X. Zhang, M. T. Eickbush, and T. H. Eickbush Role of Recombination in the Long-Term Retention of Transposable Elements in rRNA Gene Loci Genetics, November 1, 2008; 180(3): 1617 - 1626. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 D. G. Eickbush, J. Ye, X. Zhang, W. D. Burke, and T. H. Eickbush Epigenetic Regulation of Retrotransposons within the Nucleolus of Drosophila Mol. Cell. Biol., October 15, 2008; 28(20): 6452 - 6461. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 X. Zhang, J. Zhou, and T. H. Eickbush Rapid R2 Retrotransposition Leads to the Loss of Previously Inserted Copies via Large Deletions of the rDNA Locus Mol. Biol. Evol., January 1, 2008; 25(1): 229 - 237. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. Ye and T. H. Eickbush Chromatin Structure and Transcription of the R1- and R2-Inserted rRNA Genes of Drosophila melanogaster Mol. Cell. Biol., December 1, 2006; 26(23): 8781 - 8790. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
K. K. Kojima, K.-i. Kuma, H. Toh, and H. Fujiwara Identification of rDNA-Specific Non-LTR Retrotransposons in Cnidaria Mol. Biol. Evol., October 1, 2006; 23(10): 1984 - 1993. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 S. M. Christensen, A. Bibillo, and T. H. Eickbush Role of the Bombyx mori R2 element N-terminal domain in the target-primed reverse transcription (TPRT) reaction Nucleic Acids Res., November 10, 2005; 33(20): 6461 - 6468. [Abstract] [Full Text] [PDF]
|
|