Circularization analysis of minicircle sequences of Le29 isolate obtained through mapping and visualization in IGV. The compressed graphs show the alignment between paired-end Illumina reads (1), represented as horizontal lines, and the merged sequences (2), displayed along a 201 bp axis. Merged sequences were obtained by extracting the last 100 bases of each sequence and appending them to the beginning of the first 100 bases of such sequences. The bars represent coverage at each position of the axis (3). Red lines indicate forward-strand reads, and blue lines indicate reverse-strand reads. A vertical line (4) marks the junction where the ends merge, and the box (5) highlights the region where overlap is expected to verify circularity. A) Coverage of Illumina reads in a non-circularized contig. Moderate coverage is observed at the junction region, and no reads were found to be shared between both ends. B) Alignment of Illumina reads against correctly circularized contigs shows high coverage at the junction position of the merged sequence, with reads shared between both ends.

Sequence Logo represents the conserved region of minicircle sequences of T. lainsoni obtained by ONT. The graph shows the frequency of nucleotides in each minicircles multiple alignment position. Dotted lines mark conserved blocks CSB-1, CSB-2, and CSB-3. Similarly to minicircle contigs obtained with Illumina sequencing, these blocks show a high conservation level despite the higher error rate during ONT base calling.

Mapping of estimated guide RNA (gRNA) sequences to the hypervariable region (mHVR) of T. lainsoni minicircles. The number of estimated gRNAs mapped to each base position in the mHVR is shown. The distribution indicates that the estimated positions of gRNAs range from approximately 77 bp to 202 bp downstream of CSB-3.