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First published online October 24, 2008; 10.1104/pp.108.127910

Plant Physiology 148:1760-1771 (2008)
© 2008 American Society of Plant Biologists

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GENOME ANALYSIS

Replication of Nonautonomous Retroelements in Soybean Appears to Be Both Recent and Common1,[W],[OA]

Adam Wawrzynski, Tom Ashfield, Nicolas W.G. Chen, Jafar Mammadov2, Ashley Nguyen, Ram Podicheti, Steven B. Cannon, Vincent Thareau, Carine Ameline-Torregrosa, Ethalinda Cannon, Ben Chacko, Arnaud Couloux, Anita Dalwani, Roxanne Denny, Shweta Deshpande, Ashley N. Egan, Natasha Glover, Stacy Howell, Dan Ilut, Hongshing Lai, Sara Martin del Campo, Michelle Metcalf, Majesta O'Bleness, Bernard E. Pfeil, Milind B. Ratnaparkhe, Sylvie Samain, Iryna Sanders, Béatrice Ségurens, Mireille Sévignac, Sue Sherman-Broyles, Dominic M. Tucker, Jing Yi, Jeff J. Doyle, Valérie Geffroy, Bruce A. Roe, M.A. Saghai Maroof, Nevin D. Young and Roger W. Innes*

Department of Biology, Indiana University, Bloomington, Indiana 47405 (A.W., T.A., R.P., A.D., S.H., S.M.d.C., M.M., R.W.I.); Institut de Biotechnologie des Plantes, UMR CNRS 8618, INRA, Université Paris Sud, 91 405 Orsay, France (N.W.G.C., V.T., M.S., V.G.); Department of Crop and Soil Environmental Sciences, Virginia Tech, Blacksburg, Virginia 24061 (J.M., A.N., N.G., M.B.R., D.M.T., M.A.S.M.); Department of Plant Pathology, University of Minnesota, St. Paul, Minnesota 55108 (S.B.C., C.A.-T., E.C., B.C., R.D., N.D.Y.); U.S. Department of Agriculture-Agricultural Research Service and Department of Agronomy (S.B.C.), and Virtual Reality Application Center (E.C.), Iowa State University, Ames, Iowa 50011; Genoscope/CEA-Centre National de Séquençage, 91 057 Evry, France (A.C., S.S., B.S.); Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019 (S.D., H.L., M.O., I.S., J.Y., B.A.R.); L.H. Bailey Hortorium, Department of Plant Biology, Cornell University, Ithaca, New York 14853 (A.N.E., D.I., B.E.P., S.S.-B., J.J.D.); CSIRO Plant Industry, Canberra, Australian Capital Territory 2601, Australia (B.E.P.); and Division of Plant Sciences, University of Missouri, Columbia, Missouri 65211 (M.B.R.)

Retrotransposons and their remnants often constitute more than 50% of higher plant genomes. Although extensively studied in monocot crops such as maize (Zea mays) and rice (Oryza sativa), the impact of retrotransposons on dicot crop genomes is not well documented. Here, we present an analysis of retrotransposons in soybean (Glycine max). Analysis of approximately 3.7 megabases (Mb) of genomic sequence, including 0.87 Mb of pericentromeric sequence, uncovered 45 intact long terminal repeat (LTR)-retrotransposons. The ratio of intact elements to solo LTRs was 8:1, one of the highest reported to date in plants, suggesting that removal of retrotransposons by homologous recombination between LTRs is occurring more slowly in soybean than in previously characterized plant species. Analysis of paired LTR sequences uncovered a low frequency of deletions relative to base substitutions, indicating that removal of retrotransposon sequences by illegitimate recombination is also operating more slowly. Significantly, we identified three subfamilies of nonautonomous elements that have replicated in the recent past, suggesting that retrotransposition can be catalyzed in trans by autonomous elements elsewhere in the genome. Analysis of 1.6 Mb of sequence from Glycine tomentella, a wild perennial relative of soybean, uncovered 23 intact retroelements, two of which had accumulated no mutations in their LTRs, indicating very recent insertion. A similar pattern was found in 0.94 Mb of sequence from Phaseolus vulgaris (common bean). Thus, autonomous and nonautonomous retrotransposons appear to be both abundant and active in Glycine and Phaseolus. The impact of nonautonomous retrotransposon replication on genome size appears to be much greater than previously appreciated.

1 This work was supported by the National Science Foundation (Plant Genome Research Program grant no. DBI–0321664 to R.W.I., M.A.S.M., N.D.Y., B.A.R., and J.J.D. and Systematics award no. DEB–0516673 to A.N.E.) and by Genoscope/CEA-Centre National de Séquençage (grant to V.G.).

2 Present address: Trait Genetics and Technology, Dow AgroSciences LLC, Indianapolis, IN 46268.

The author responsible for distribution of materials integral to the findings presented in this article in accordance with the policy described in the Instructions for Authors (www.plantphysiol.org) is: Roger W. Innes (rinnes{at}indiana.edu).

[W] The online version of this article contains Web-only data.

[OA] Open access articles can be viewed online without a subscription.

www.plantphysiol.org/cgi/doi/10.1104/pp.108.127910

* Corresponding author; e-mail rinnes{at}indiana.edu.

Received August 10, 2008; accepted October 22, 2008; published October 24, 2008.

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