T-DNAreader: fast and precise identification of T-DNA insertion sites in plant genomes using RNA sequencing data
Abstract 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 sometimes integrate during a single transformation,...
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| Main Authors: | , |
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| Format: | Article |
| Language: | English |
| Published: |
BMC
2025-07-01
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| Series: | Genome Biology |
| Subjects: | |
| Online Access: | https://doi.org/10.1186/s13059-025-03655-x |
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| Summary: | Abstract 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 sometimes integrate during a single transformation, necessitating the development of tools to elucidate the T-DNA insertion sites (TISs). Here, we present T-DNAreader, which identifies TISs from RNA sequencing data with high precision, sensitivity, and speed, outperforming existing tools. T-DNAreader enables the efficient and reliable identification of TISs within transcribed regions and standardizes the characterization of T-DNA-containing transgenic plants, which can be expanded to various organisms containing T-DNA. |
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| ISSN: | 1474-760X |