Fig. 2

Methodologies to determinate the chromosomal copy number in T. cruzi strains. To estimate the chromosome ploidy of T. cruzi strains, two approaches were evaluated by mapping reads from the Y strain on the 41 CL Brener chromosomes. a The Whole Chromosome Ploidy Estimations (WCPE) predicts the ploidy based on the mean coverage of the whole-chromosome sequence. b The single-copy genes ploidy estimations (SCoPE) predict the chromosomal ploidy based only on the coverage of the 1563 Esmo-like/Non-Esmo single-copy genes present in each chromosome. The read depth was scaled to give a value of 2 for disomic chromosomes. c The 41 T. cruzi chromosome gene distribution is shown. Multicopy gene families are represented as blue boxes and the hypothetical and housekeeping genes as black boxes. The red arrows highlight the chromosomes with a higher content of multigene families or with the largest proportion of gap regions. Chromosomes with a higher density of multigene families or that present large gap regions tend to have a biased lower predicted ploidy in the WCPE when compared to the SCoPE method. Similar results were obtained for all the other strains evaluated