Binary vector origin predictably determines Agrobacterium -mediated transformation outcome across eukaryotic kingdoms

Agrobacterium -mediated transformation (AMT) is the primary means of genetic engineering in plants and many fungi, but the factors that control transformation outcomes—efficiency, transgene insertion number, and transgene integrity—remain poorly characterized. Although transformation outcomes dictate an event’s potential utility in both industrial and academic contexts, AMT remains largely unoptimized for these metrics. Here, we systematically analyze the impact of the transgene-harboring binary vector on transformation outcomes across plant and fungal species. Through a comparison of different plasmid origin of replication (ORI) families and engineered copy number variants, our results reveal that the ORI family—not plasmid copy number—dictates T-DNA insertion number, backbone inclusion, and transformation efficiency, while plasmid copy number tuning alters efficiency without changing ORI family-specific signatures. Independent of plasmid copy number across kingdoms, the most widely used pVS1 ORI-based vectors (e.g. pCambia) result in significantly more insertions per transformant and high levels of transgene silencing compared to the less-utilized pSa ORI family, which enriches for more uniform single insertion events. Furthermore, we demonstrate that ORI-dependent transformation outcomes in yeast predictably reflect those in Arabidopsis . Together, these results lay the foundation for future binary vector design aimed at achieving more predictable, controllable, and optimized transformation outcomes across diverse eukaryotic hosts.