Diversity of DcMaster-like elements of the PIF/Harbinger superfamily in the carrot genome.

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 previously described, relatively highly abundant miniature inverted repeat element (MITE) family Krak (ca. 3,600 copies, ca. 80% intra-family similarity), three other families, i.e. 1.1 kb long KrakL1 (ca. 3,000 copies, ca. 98% intra-family similarity), 1.2 kb long KrakL2 (a single identified element, 71.1% similar to KrakL1 consensus), and 2.2 kb long Midi (few elements, 99% intra-family similarity), were revealed. The fact that all members within each of the newly found families were almost identical in their sequence suggests their very recent activity. The families differed in terms of their similarity to the canonical DcMaster element. They also differed in copy number, from just a few copies of Midi 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 Daucus carota.