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doi:10.1534/genetics.106.062752
A more recent version of this article appeared on December 1, 2006.
REGULAR RESEARCH PAPERS |
The transposable element landscape of the model legume Lotus japonicus
Dawn Holligan 1, Xiaoyu Zhang 2, Ning Jiang 3, Ellen J Pritham 4 and Sue Wessler 1*
1 University of Georgia
2 University of California Los Angeles
3 Michigan State University
4 University of Texas at Arlington
* To whom correspondence should be addressed. E-mail: sue{at}plantbio.uga.edu.
Submitted on June 28, 2006
Revised on August 17, 2006
Accepted on 18 September 2006
The largest component of plant and animal genomes characterized to date is transposable elements. 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 genome wide 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 more than one thousand 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.
Key Words: L.japonicus, Pack-MULEs, Sireviruses, genome evolution, polymorphism
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