Fig. 2

Schematic illustration of assembly problems based on read length. (A) Using short Illumina reads, the assembly of a single TALE may be ambiguous due to highly conserved tandem repeats, which often differ only in their RVD di-codon indicated by coloured boxes. Starting from the same set of Illumina reads, two alternative assemblies are consistent with the reads. Using long read technologies, however, the bottom assembly may be identified as the correct one. (B) Even using longer reads spanning complete TALEs, the organization and order of TALE within clusters may be ambiguous due to highly conserved N-terminus, C-terminus and linker sequence between TALEs. Here, very long ONT reads spanning complete TALE clusters are capable of resolving the arrangement of TALEs in large clusters