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Background  Integration of T-DNA into plant genomes via  Agrobacterium  may interrupt gene structure and generate numerous mutants. The T-DNA caused mutants are valuable materials for understanding T-DNA integration model in plant research. T-DNA integration in plants is complex and still largely unknown. In this work, we reported that multiple T-DNA fragments caused chromosomal translocation and deletion in a birch ( Betula platyphylla × B. pendula ) T-DNA mutant  yl .    Results  We performed PacBio genome resequencing for  yl  and the result revealed that two ends of a T-DNA can be integrated into plant genome independently because the two ends can be linked to different chromosomes and cause chromosomal translocation. We also found that these T-DNA were connected into tandem fragment regardless of direction before integrating into plant genome. In addition, the integration of T-DNA in  yl  genome also caused several chromosomal fragments deletion. We then summarized three cases for T-DNA integration model in the  yl  genome. (1) A T-DNA fragment is linked to the two ends of a double-stranded break (DSB); (2) Only one end of a T-DNA fragment is linked to a DSB; (3) A T-DNA fragment is linked to the ends of different DSBs. All the observations in the  yl  genome supported the DSB repair model.    Conclusions  In this study, we showed a comprehensive genome analysis of a T-DNA mutant and provide a new insight into T-DNA integration in plants. These findings would be helpful for the analysis of T-DNA mutants with special phenotypes.    Electronic supplementary material  The online version of this article (10.1186/s12864-019-5636-y) contains supplementary material, which is available to authorized users.

Comprehensive characterization of T-DNA integration induced chromosomal rearrangement in a birch T-DNA mutant