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Chagas disease is a complex illness caused by the protozoan  Trypanosoma cruzi  displaying highly diverse clinical outcomes. In this sense, the genome sequence elucidation and comparison between strains may lead to disease understanding. Here, two new  T. cruzi  strains, have been sequenced, Y using Illumina and Bug2148 using PacBio, assembled, analyzed and compared with the  T. cruzi  annotated genomes available to date. The assembly stats from the new sequences show effective improvement of  T. cruzi  genome over the actual ones. Such as, the largest contig assembled (1.3 Mb in Bug2148) in  de novo  attempts and the highest mean assembly coverage (71X for Y). Our analysis reveals a new genomic expansion and greater complexity for those multi-copy gene families related to infection process and disease development, such as Trans-sialidases, Mucins and Mucin Associated Surface Proteins, among others. On one side, we demonstrate that multi-copy gene families are located near telomeric regions of the “chromosome-like” 1.3 Mb contig assembled of Bug2148, where they likely suffer high evolutive pressure. On the other hand, we identified several strain-specific single copy genes that might help to understand the differences in infectivity and physiology among strains. In summary, our results indicate that  T. cruzi  has a complex genomic architecture that may have promoted its evolution.

Genomic assemblies of newly sequenced Trypanosoma cruzi strains reveal new genomic expansion and greater complexity