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Originally published as Genetics Published Articles Ahead of Print on October 8, 2006.
Genetics, Vol. 174, 2215-2228, December 2006, Copyright © 2006
doi:10.1534/genetics.106.062752
The Transposable Element Landscape of the Model Legume Lotus japonicus
Dawn Holligan*,
Xiaoyu Zhang*,1,
Ning Jiang
,
Ellen J. Pritham*,2 and
Susan R. Wessler*,3
* Department of Plant Biology, University of Georgia, Athens, Georgia 30602 and Department of Horticulture, Michigan State University, East Lansing, Michigan 48824
3 Corresponding author: Department of Plant Biology, 2502 Miller Plant Sciences Bldg., University of Georgia, Athens, GA 30602.
E-mail: sue{at}plantbio.uga.edu
The largest component of plant and animal genomes characterized to date is transposable elements (TEs). The availability of a significant amount of Lotus japonicus genome sequence has permitted for the first time a comprehensive study of the TE landscape in a legume species. Here we report the results of a combined computer-assisted and experimental analysis of the TEs in the 32.4 Mb of finished TAC clones. While computer-assisted analysis facilitated a determination of TE abundance and diversity, the availability of complete TAC sequences permitted identification of full-length TEs, which facilitated the design of tools for genomewide experimental analysis. In addition to containing all TE types found in previously characterized plant genomes, the TE component of L. japonicus contained several surprises. First, it is the second species (after Oryza sativa) found to be rich in Pack-MULEs, with >1000 elements that have captured and amplified gene fragments. In addition, we have identified what appears to be a legume-specific MULE family that was previously identified only in fungal species. Finally, the L. japonicus genome contains many hundreds, perhaps thousands of Sireviruses: Ty1/copia-like elements with an extra ORF. Significantly, several of the L. japonicus Sireviruses have recently amplified and may still be actively transposing.
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