The widely used Nicotiana benthamiana 16c line has an unusual T-DNA integration pattern including a transposon sequence

• Published in: PloS one Vol. 12; no. 2; p. e0171311
• Main Authors: Philips, Joshua G, Naim, Fatima, Lorenc, Michał T, Dudley, Kevin J, Hellens, Roger P, Waterhouse, Peter M
• Format: Journal Article
• Language: English
• Published: United States Public Library of Science 23.02.2017; Public Library of Science (PLoS)
• Subjects: Aequorea victoria; Agrobacterium tumefaciens; Assembly; Bacteria; Base sequence; Biology; Biology and Life Sciences; Cell lines; Deoxyribonucleic acid; DNA; DNA methylation; DNA Transposable Elements; DNA, Bacterial - genetics; Epigenetics; Fluorescence; Gene expression; Gene Library; Gene mapping; Gene sequencing; Genetic aspects; Genetic engineering; Genomes; Green fluorescent protein; Green fluorescent proteins; Green Fluorescent Proteins - genetics; Heredity; High-Throughput Nucleotide Sequencing; Nicotiana - genetics; Nicotiana benthamiana; Nucleotide sequence; Plants, Genetically Modified - genetics; Proteins; Research and Analysis Methods; T-DNA; Tobacco (Plant); Transgenic plants; Transposase gene; Transposons; Queensland Australia; Australia
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0171311

Nicotiana benthamiana is employed around the world for many types of research and one transgenic line has been used more extensively than any other. This line, 16c, expresses the Aequorea victoria green fluorescent protein (GFP), highly and constitutively, and has been a major resource for visualising the mobility and actions of small RNAs. Insights into the mechanisms studied at a molecular level in N. benthamiana 16c are likely to be deeper and more accurate with a greater knowledge of the GFP gene integration site. Therefore, using next generation sequencing, genome mapping and local alignment, we identified the location and characteristics of the integrated T-DNA. As suggested from previous molecular hybridisation and inheritance data, the transgenic line contains a single GFP-expressing locus. However, the GFP coding sequence differs from that originally reported. Furthermore, a 3.2 kb portion of a transposon, appears to have co-integrated with the T-DNA. The location of the integration mapped to a region of the genome represented by Nbv0.5scaffold4905 in the www.benthgenome.com assembly, and with less integrity to Niben101Scf03641 in the www.solgenomics.net assembly. The transposon is not endogenous to laboratory strains of N. benthamiana or Agrobacterium tumefaciens strain GV3101 (MP90), which was reportedly used in the generation of line 16c. However, it is present in the popular LBA4404 strain. The integrated transposon sequence includes its 5' terminal repeat and a transposase gene, and is immediately adjacent to the GFP gene. This unexpected genetic arrangement may contribute to the characteristics that have made the 16c line such a popular research tool and alerts researchers, taking transgenic plants to commercial release, to be aware of this genomic hitchhiker.