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Published on October 24, 2008; 10.1104/pp.108.127910

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Received August 10, 2008
Accepted October 22, 2008

Replication of Non-autonomous Retroelements in Soybean Appears to be Both Recent and Common

Adam Wawrzynski , Tom Ashfield , Nicolas W. G. Chen , Jafar Mammadov , 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 , Beatrice Segurens , Mireille Sevignac , Sue Sherman-Broyles , Dominic M. Tucker , Jing Yi , Jeff J. Doyle , Valerie Geffroy , Bruce A. Roe , M.A. Saghai Maroof , Nevin D. Young , and Roger W. Innes *

Department of Biology, Indiana University, Bloomington, Indiana 47405; Institut de Biotechnologie des Plantes, UMR CNRS 8618, INRA, Universite Paris Sud, 91 405 Orsay, France; Virginia Tech, Blacksburg, Virginia 24061; Department of Plant Pathology, University of Minnesota, St. Paul, Minnesota 55108; USDA-ARS and Department of Agronomy, Iowa State University, Ames, Iowa 50011; Virtual Reality Application Center, Iowa State University, Ames, Iowa 50011; Genoscope/CEA-Centre National de Sequencage, 91 057 Evry, France; Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019; L.H. Bailey Hortorium, Department of Plant Biology, Cornell University, Ithaca, New York 14853; CSIRO Plant Industry, Canberra, ACT 2601 Australia; Division of Plant Sciences, University of Missouri, Columbia, Missouri 65211

* Corresponding author; email: rinnes{at}indiana.edu.

Retrotransposons and their remnants often constitute more than 50% of higher plant genomes. Although extensively studied in monocot crops such as maize and rice, 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 non-autonomous 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 G. 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 non-autonomous retrotransposons appear to be both abundant and active in Glycine and Phaseolus. The impact of non-autonomous retrotransposon replication on genome size appears to be much greater than previously appreciated.






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