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MBE Advance Access originally published online on December 22, 2004
Molecular Biology and Evolution 2005 22(4):845-855; doi:10.1093/molbev/msi069
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Molecular Biology and Evolution vol. 22 no. 4 © Society for Molecular Biology and Evolution 2004; all rights reserved.

Research Article

Structure, Divergence, and Distribution of the CRR Centromeric Retrotransposon Family in Rice

Kiyotaka Nagaki*,{dagger}, Pavel Neumann{ddagger}, Dongfen Zhang§, Shu Ouyang||, C. Robin Buell||, Zhukuan Cheng§ and Jiming Jiang*

* Department of Horticulture, University of Wisconsin-Madison; {dagger} Research Institute for Bioresources, Okayama University, Kurashiki, Japan; {ddagger} Institute of Plant Molecular Biology, Ceske Budejovice, Czech Republic; § Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China; and || The Institute for Genomic Research, Rockville, Maryland

E-mail: jjiang1{at}wisc.edu.

The centromeric retrotransposon (CR) family in the grass species is one of few Ty3-gypsy groups of retroelements that preferentially transpose into highly specialized chromosomal domains. It has been demonstrated in both rice and maize that CRR (CR of rice) and CRM (CR of maize) elements are intermingled with centromeric satellite DNA and are highly concentrated within cytologically defined centromeres. We collected all of the CRR elements from rice chromosomes 1, 4, 8, and 10 that have been sequenced to high quality. Phylogenetic analysis revealed that the CRR elements are structurally diverged into four subfamilies, including two autonomous subfamilies (CRR1 and CRR2) and two nonautonomous subfamilies (noaCRR1 and noaCRR2). The CRR1/CRR2 elements contain all characteristic protein domains required for retrotransposition. In contrast, the noaCRR elements have different structures, containing only a gag or gag-pro domain or no open reading frames. The CRR and noaCRR elements share substantial sequence similarity in regions required for DNA replication and for recognition by integrase during retrotransposition. These data, coupled with the presence of young noaCRR elements in the rice genome and similar chromosomal distribution patterns between noaCRR1 and CRR1/CRR2 elements, suggest that the noaCRR elements were likely mobilized through the retrotransposition machinery from the autonomous CRR elements. Mechanisms of the targeting specificity of the CRR elements, as well as their role in centromere function, are discussed.

Key Words: bacterial artificial chromosomes • centromeric retrotransposon • long terminal repeats • rice


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