RRC ID 2382
Author Holligan D, Zhang X, Jiang N, Pritham EJ, Wessler SR.
Title The transposable element landscape of the model legume Lotus japonicus.
Journal Genetics
Abstract 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.
Volume 174(4)
Pages 2215-28
Published 2006-12
DOI 10.1534/genetics.106.062752
PII genetics.106.062752
PMID 17028332
PMC PMC1698628
MeSH Chromosome Mapping Chromosomes, Plant DNA Transposable Elements / genetics* DNA, Plant Databases, Factual Fabaceae / genetics* Genome, Plant Lotus / genetics* Models, Biological Open Reading Frames Phylogeny Polymorphism, Genetic
IF 3.564
Times Cited 60
Lotus / Glycine Miyakojima MG-20 Gifu B-129