The complex architecture of plant T-DNA transgene insertions
About Todd Michael
Dr. Todd Michael is Professor and Director of Informatics at the J. Craig Venter Institute (JCVI) in San Diego, CA USA. At JCVI, Dr. Michael’s group builds genome sequencing, editing and analysis tools with a specific focus on developing synthetic plants. Current projects include sequencing minimal and specialized plant genomes, computationally designing a minimal plant genome, booting-up plant artificial chromosomes, and leveraging nanopore sequencing for complete genomes and epigenomic analysis.
Jupe, F. et al. The complex architecture of plant transgene insertions. bioRxiv 282772 (2018). doi:10.1101/282772
Michael, T. P. et al. High contiguity Arabidopsis thaliana genome assembly with a single nanopore flow cell. Nature Communications 9, (2018).
Over the last 35 years the soil bacterium Agrobacterium tumefaciens has been used as the workhorse in the production of transgenic plants through the replacement of its native tumor-inducing plasmid elements with customizable cassettes that enable the random integration of a Transfer DNA (T-DNA) sequence into any plant genome. Due to previous limitations in sequencing read lengths, the architecture of these T-DNA insertions has gone largely uncharacterized. We leveraged Oxford Nanopore Technologies long-reads in combination with optical maps to characterize T-DNA insertions, ranging from 27 to 236 kilobases in the model plant Arabidopsis thaliana. We generated a higher quality reference assembly, which corrected 83% of non-centromeric misassemblies in the platinum hand-curated TAIR10 assembly. For two segregating T-DNA lines we resolved structures up to 36 kb and revealed large-scale translocations events. This unprecedented nucleotide-level definition of T-DNA insertions enabled the characterization of the epigenomic status associated with the insertions.