Submitted to: Genetica
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 5/28/2008
Publication Date: 7/3/2008
Publication URL: http://www.ncbi.nlm.nih.gov/pubmed/18535910
Citation: Grzebelus, D., Simon, P.W. 2008. Diversity of DcMaster-like elements of the PIF/Harbinger superfamily in the carrot genome. Genetica. Available: http://www.ncbi.nlm.nih.gov/pubmed/18535910. Interpretive Summary: Transposable elements (TEs) are small pieces of DNA capable of changing their localization on chromosomes. They can constitute a significant portion (10 to 80%) of plant genomes. The PIF/Harbinger superfamily of TEs occurs in carrots as well as corn and alfalfa. In this study, we present the experimental evidence for the presence of other groups of DcMaster-like elements in the carrot genome which are variable in size but similar in DNA sequence to suggest they have been moving in the carrot genome recently. This research is of interest to other carrot genetics researchers and plant molecular biologists in general. Sometimes mobile DNA can cause mutations and if that is found to occur, this will be interesting to plant breeders as well.
Technical Abstract: Transposable elements constitute a significant fraction of plant genomes. Both autonomous and non-autonomous elements of the DcMaster family, residing in the carrot genome, were described previously. DcMaster elements were classified as members of the PIF/Harbinger superfamily. In the present paper we report on the identification of other groups of DcMaster-like elements. Beside the relatively highly abundant Krak family of miniature inverted repeat elements (MITEs), three other families, i.e. 1.1 kb long KrakL1, 1.2 kb long KrakL2, and 2.2 kb long KrakXL, were revealed. Interestingly, all members within each of the newly found families were almost identical in their sequence, suggesting their very recent activity. The families differed in terms of their similarity to the canonical DcMaster element, which likely reflected their evolution. They also differed in copy number, from just a few copies of KrakXL to few thousand copies of Krak. A modification of the DcMaster Transposon Display (DcMTD) marker system, targeted specifically towards Krak elements, was used to investigate their insertion polymorphism. It was shown that Krak insertion sites, similarly to those of the DcMaster elements, were highly polymorphic between the wild and the cultivated D. carota.