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United States Department of Agriculture

Agricultural Research Service

Title: Master - a Novel Family of Pif/harbinger-Like Transposable Elements Identified in Carrot (Daucus Carota L.)

Authors
item Grzebelus, Dariusz - AG UNIV OF KRAKOW POLAND
item Yau, Yuan-Yeu - UNIV OF CA BERKELEY
item Simon, Philipp

Submitted to: Molecular Genetics and Genomics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: January 10, 2006
Publication Date: February 16, 2006
Citation: Grzebelus, D., Yau, Y., Simon, P.W. 2006. Master - a novel family of PIF/Harbinger-like transposable elements identified in carrot (Daucus carota L.). Molecular Genetics and Genomics. 275:450-459.

Interpretive Summary: While the relative location of genes on chromosomes is generally regarded as fixed and unchanging fro an organism, examples of mobile DNA elements have been discovered for several plant, animal, and microbial species. We recently discovered a part of a mobile DNA element in carrot ant this research reports the full element, the first discovered for carrot. This information is of interest to biologists studying genetic organization of chromosomes, and to researchers studying carrot genetics.

Technical Abstract: Two new families of transposable elements, DcMaster and DcMITEs, were identified in the carrot genome. Two members of the DcMaster family were thoroughly characterized and differed by ~1.9 kb deletion. They had 22 bp imperfect terminal inverted repeats and formed 3 bp target site duplications. The larger 4432 bp element, DcMaster-a, contains an open reading frame coding for a putative transposase with complete DDE domain characteristics of plant class II transposable elements belonging to PIF/Harbinger superfamily. DcMaster is the first PIF/Harbinger-like element identified and characterized in any dicot species other than Arabidopsis thaliana. Under ten copies of the DcMaster element containing the DDE domain occur in genomes of carrot and other Apiaceae, but more copies with internal deletions or insertions may occur. DcMaster elements were associated with putative coding regions in 8 of 14 identified insertion sites. PCR amplification of carrot genomic DNA using a primer complementary to TIRs of DcMaster gave products < 400 bp in size. We speculate that these may all represent a MITE-like family of transposable elements that we named DcMITEs. To our knowledge this is the first report on identification of a novel MITE family based directly on sequence information from class II transposable elements.

Last Modified: 10/24/2014