Agrobacterium evolved the capability to transfer a DNA fragment (T-DNA) of their own genome into the nuclear genome of plants (Gelvin, 2017). This natural process of interkingdom horizontal gene transfer (HGT) contributes to exploitation of the plant host by Agrobacterium bacterial pathogens (Gonzalez-Mula et al., 2018 and 2019). This unique HGT process also inspired the development of a wide spectrum of tools and technologies dedicated to genetic engineering of plants and some other eukaryotes (Sardesai & Subramanyam, 2018). In spite of a popular usage of these tools in basic science and genetic engineering, the ultimate step of the HGT process, namely integration of the T-DNA into nuclear genome of plants remains in a grey zone of knowledge (Singer, 2018). In this issue of New phytologist, Nishizawa-Yokoi et al. (pp. 000-000) suggest that host factors controlling TDNA integration are different in somatic and germinal plnt cells. This article invites the scientific community to debate about the existence of different molecular machineries allowing T-DNA integration in plant genome.