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Plant Cell Advance Online Publication
Published on January 15, 2010; 10.1105/tpc.109.068775

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Received May 18, 2009
Returned for revision October 11, 2009
Accepted October 23, 2009

Bifurcation and Enhancement of Autonomous-Nonautonomous Retrotransposon Partnership through LTR Swapping in Soybean

Jianchang Du 1, Zhixi Tian 1, Nathan J. Bowen 2, Jeremy Schmutz 3, Randy C. Shoemaker 4, and Jianxin Ma 1*

1 Department of Agronomy, Purdue University, West Lafayette, Indiana 47907
2 School of Biology, Georgia Institute of Technology, Atlanta, Georgia 30332
3 Hudson Alpha Institute, Hunstville, Alabama 35806
4 U.S. Department of Agriculture–Agricultural Research Service, Corn Insect and Crop Genetics Research Unit, Ames, Iowa 50011

* To whom correspondence should be addressed. E-mail: maj{at}purdue.edu.

Long terminal repeat (LTR) retrotransposons, the most abundant genomic components in flowering plants, are classifiable into autonomous and nonautonomous elements based on their structural completeness and transposition capacity. It has been proposed that selection is the major force for maintaining sequence (e.g., LTR) conservation between nonautonomous elements and their autonomous counterparts. Here, we report the structural, evolutionary, and expression characterization of a giant retrovirus-like soybean (Glycine max) LTR retrotransposon family, SNARE. This family contains two autonomous subfamilies, SAREA and SAREB, that appear to have evolved independently since the soybean genome tetraploidization event ~13 million years ago, and a nonautonomous subfamily, SNRE, that originated from SAREA. Unexpectedly, a subset of the SNRE elements, which amplified from a single founding SNRE element within the last ~3 million years, have been dramatically homogenized with either SAREA or SAREB primarily in the LTR regions and bifurcated into distinct subgroups corresponding to the two autonomous subfamilies. We uncovered evidence of region-specific swapping of nonautonomous elements with autonomous elements that primarily generated various nonautonomous recombinants with LTR sequences from autonomous elements of different evolutionary lineages, thus revealing a molecular mechanism for the enhancement of preexisting partnership and the establishment of new partnership between autonomous and nonautonomous elements.






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