Tags

Type your tag names separated by a space and hit enter

Long-term inheritance of the 28S rDNA-specific retrotransposon R2.
Mol Biol Evol. 2005 Nov; 22(11):2157-65.MB

Abstract

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.

Authors+Show Affiliations

Department of Integrated Biosciences, Graduate School of Frontier Sciences, University of Tokyo, Chiba, Japan.No affiliation info available

Pub Type(s)

Comparative Study
Journal Article
Research Support, Non-U.S. Gov't

Language

eng

PubMed ID

16014872

Citation

Kojima, Kenji K., and Haruhiko Fujiwara. "Long-term Inheritance of the 28S rDNA-specific Retrotransposon R2." Molecular Biology and Evolution, vol. 22, no. 11, 2005, pp. 2157-65.
Kojima KK, Fujiwara H. Long-term inheritance of the 28S rDNA-specific retrotransposon R2. Mol Biol Evol. 2005;22(11):2157-65.
Kojima, K. K., & Fujiwara, H. (2005). Long-term inheritance of the 28S rDNA-specific retrotransposon R2. Molecular Biology and Evolution, 22(11), 2157-65.
Kojima KK, Fujiwara H. Long-term Inheritance of the 28S rDNA-specific Retrotransposon R2. Mol Biol Evol. 2005;22(11):2157-65. PubMed PMID: 16014872.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Long-term inheritance of the 28S rDNA-specific retrotransposon R2. AU - Kojima,Kenji K, AU - Fujiwara,Haruhiko, Y1 - 2005/07/13/ PY - 2005/7/15/pubmed PY - 2006/6/6/medline PY - 2005/7/15/entrez SP - 2157 EP - 65 JF - Molecular biology and evolution JO - Mol. Biol. Evol. VL - 22 IS - 11 N2 - 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. SN - 0737-4038 UR - https://www.unboundmedicine.com/medline/citation/16014872/Long_term_inheritance_of_the_28S_rDNA_specific_retrotransposon_R2_ L2 - https://academic.oup.com/mbe/article-lookup/doi/10.1093/molbev/msi210 DB - PRIME DP - Unbound Medicine ER -