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Systematic Biology 2006 55(6):949-956; doi:10.1080/10635150601047843
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© 2006 Society of Systematic Biologists

Short Interspersed Elements (SINEs) in Plants: Origin, Classification, and Use as Phylogenetic Markers

Jean-Marc Deragon1 and Xiaoyu Zhang2

1 CNRS UMR6547, GDR2157 Biomove, Université Blaise Pascal 24 Avenue des Landais, 63177, Aubière, France E-mail: j-marc.deragon{at}univ-bpclermont.fr
2 Department of Molecular, Cell, and Developmental Biology, University of California Los Angeles, California, 90095-1606, USA

Edited by Andrew Shedlock: Associate Editor


  Abstract

Short interspersed elements (SINEs) are a class of dispersed mobile sequences that use RNA as an intermediate in an amplification process called retroposition. The presence-absence of a SINE at a given locus has been used as a meaningful classification criterion to evaluate phylogenetic relations among species. We review here recent developments in the characterisation of plant SINEs and their use as molecular makers to retrace phylogenetic relations among wild and cultivated Oryza and Brassica species. In Brassicaceae, further use of SINE markers is limited by our partial knowledge of endogenous SINE families (their origin and evolution histories) and by the absence of a clear classification. To solve this problem, phylogenetic relations among all known Brassicaceae SINEs were analyzed and a new classification, grouping SINEs in 15 different families, is proposed. The relative age and size of each Brassicaceae SINE family was evaluated and new phylogenetically supported subfamilies were described. We also present evidence suggesting that new potentially active SINEs recently emerged in Brassica oleracea from the shuffling of preexisting SINE portions. Finally, the comparative evolution history of SINE families present in Arabidopsis thaliana and Brassica oleracea revealed that SINEs were in general more active in the Brassica lineage. The importance of these new data for the use of Brassicaceae SINEs as molecular markers in future applications is discussed.

Keywords: Arabidopsis; Brassica; molecular markers; retroposon; retrotransposon; rice; SINE; transposable element; transposon

Received January 18, 2006; Revised March 28, 2006; Accepted April 16, 2006
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