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Background   Trypanosoma cruzi  is a protozoan parasite and the etiologic agent of Chagas disease, an important public health problem in Latin America.  T. cruzi  is diploid, almost exclusively asexual, and displays an extraordinarily diverse population structure both genetically and phenotypically. Yet, to date the genotypic diversity of  T. cruzi  and its relationship, if any, to biological diversity have not been studied at the whole genome level.    Results  In this study, we used whole genome oligonucleotide tiling arrays to compare gene content in biologically disparate  T. cruzi  strains by comparative genomic hybridization (CGH). We observed that  T. cruzi  strains display widespread and focal copy number variations (CNV) and a substantially greater level of diversity than can be adequately defined by the current genetic typing methods. As expected, CNV were particularly frequent in gene family-rich regions containing mucins and trans-sialidases but were also evident in core genes. Gene groups that showed little variation in copy numbers among the strains tested included those encoding protein kinases and ribosomal proteins, suggesting these loci were less permissive to CNV. Moreover, frequent variation in chromosome copy numbers were observed, and chromosome-specific CNV signatures were shared by genetically divergent  T. cruzi  strains.    Conclusions  The large number of CNV, over 4,000, reported here uphold at a whole genome level the long held paradigm of extraordinary genome plasticity among  T. cruzi  strains. Moreover, the fact that these heritable markers do not parse  T. cruzi  strains along the same lines as traditional typing methods is strongly suggestive of genetic exchange playing a major role in  T. cruzi  population structure and biology.

bmc genomics

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