Search

Additional file 1:Microsoft PowerPoint file of theCGHViewer view of T. cruzi chromosome 35 showing the CNV generated by knockout of one copy each of ECH1 and ECH2 (enoyl-CoA hydratase/isomerase family protein; Tc00.1047053511529.160, Tc00.1047053511529.150). Each dot represents an oligonucleotide probe. The CL-Brener strain, which was used as the reference strain for genome sequencing, is hybrid, thus probes were designed to non-Esmeraldo (non-Esm) sequences (blue), Esmeraldo-like (Esm) sequences (green), non-Esm gene family sequences (black), and Esm gene family sequences (gray). Positive log2 ratios of signal intensities (wild type strain/knockout strain) represent deletion in the knockout strain and negative log2 ratios represent amplification in the knockout strain, relative to wt T. cruzi. Units for the X axis (Position) are base pairs. Inset in panel A is the GBrowse view of the locus (ECH genes purple circle). Panel B is a close-up view of the locus on chromosome 35. (PPT 780 KB)

Additional file of Widespread, focal copy number variations (CNV) and whole chromosome aneuploidies in Trypanosoma cruzi strains revealed by array comparative genomic hybridization

Additional File 2:PowerPoint file of all of the array data ordered by chromosome. Representative plots from 16 hybridizations for each T. cruzi chromosome. Each dot represents an oligonucleotide probe. The CL-Brener strain, which was used as the reference strain for genome sequencing, is hybrid, thus probes were designed to non-Esmeraldo (non-Esm) sequences (blue), Esmeraldo-like (Esm) sequences (green), non-Esm gene family sequences (black), and Esm gene family sequences (gray). In each panel positive log2 ratios of signal intensities (test strain/reference) represent amplification in the test strain and negative log2 ratios represent deletion in the test strain, relative to CL-Brener, which was the reference strain in all hybridizations. Boxed regions were the features selected for chromosome typing as explained in Figure 3. The different patterns observed for each chromosome are displayed at the bottom with letters corresponding to the typing letters in Figure 3. Blue boxes denote lower copy number in the test strain versus the reference strain, red boxes higher copy number in the test strain, and black boxes equal copy number in the test and reference strains. In each case for each chromosome, the CL-Brener type was the default type "A." Also, while two strains may have been assigned to the same CNV signature type for a given chromosome, they were not necessarily identical for that chromosome, as not every single CNV for every single chromosome was used in the typing (such an analysis would render every chromosome for every strain unique and make finding common patterns impossible). Note that chromosomes 4, 5, 18, 28, and 29 did not present sufficiently informative typing regions. Thus, all strains were type "A" for these chromosomes. Also, the CNV were haplotype specific. Therefore, in some cases this made the up or down calls (box color) appear incorrect, especially if the log2ratio for the feature was off the scale making it appear as if the boxed region is referring to the other haplotype. For example see PalDa for chromosome 8. In the boxed region the green (Esm) probes appear to be up yet the box is blue, indicating lower copy number, because the feature refers to non-Esm probes which are off the scale of the figure. Lastly, the boxes are guides to identifying the CNV used for typing, but they do not represent the exact bounds of those typing regions. In some cases due to the scale of the figure CNV that are close to the typing CNV appear to be part of the typing CNV. (PPT 16 MB)