The DNA sequences of T-DNA junctions suggest that complex T-DNA loci are formed by a recombination process resembling T-DNA integration

After Agrobacterium-mediated plant transformation, multiple T-DNAs frequent ly integrate at the same position in the plant genome, resulting in the for mation of inverted and direct repeats. Because these inverted repeats canno t be amplified and analyzed by PCR, Arabidopsis root cells were co-transfor med with two different T-DNAs with distinct sequences adjacent to the T-DNA borders. Nine direct or inverted T-DNA border junctions were analyzed at t he sequence level. Precise end-to-end fusions were found between two right border ends, whereas imprecise fusions and filler DNA were present in T-DNA linkages containing a left border end. The results suggest that end-to-end ligation of double-stranded T-DNAs occurs especially between right T-DNA e nds and that illegitimate recombination on the basis of microhomology, dele tions, repair activities and insertions of filler DNA is involved in the fo rmation of left border T-DNA junctions. Therefore, a similar illegitimate r ecombination mechanism is proposed that is involved in the formation of com plex T-DNA inserts as well as in the integration of the T-DNA in the plant genome.