T-DNAreader: fast and precise identification of T-DNA insertion sites using RNA-seq data

Agrobacterium-mediated plant transformation, which enables the delivery of DNA using transfer DNA (T-DNA) binary vectors, is an essential technique in plant research. T-DNAs randomly integrate into the host genome and multiple T-DNAs can integrate in a single transformation event, necessitating the development of efficient, reliable tools to identify the T-DNA insertion sites (TISs). Here, we developed T-DNAreader to identify TISs from RNA-sequencing (RNA-seq) data with high precision, sensitivity, and speed, outperforming existing tools. T-DNAreader detected previously unknown TISs in characterized mutant plants. Overall, T-DNAreader enables the simple identification of TISs within transcribed regions and standardizes the characterization of T-DNA-containing transgenic plants.