Genetically modified (GM) plants have to be analysed regarding biosafety, before they can be imported or cultivated. An important part is analysis of the DNA sequence of the inserted transgenes and the flanking DNA in the plant. This was done by means of conventional techniques, such as Southern blotting. However, in this project we will evaluate the use of Next Generation Sequencing (NGS) as a more accurate alternative. We already sequenced transgenic and non-transgenic tomato and Arabidopsis thaliana plants using a HiSeq paired end strategy. The
student is challenged to make de novo assemblies to identify in silico the number, nature and position for the inserted DNA fragments and the flanking plant DNA. These assemblies will be compared with PacBio sequences of the inserts.
Information at Gabino Sanchez Perez email@example.com, Henk Schouten firstname.lastname@example.org, or Elio Schijlen email@example.com