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Background   Trypanosoma cruzi , the etiologic agent of Chagas disease, is currently divided into six discrete typing units (DTUs), named TcI–TcVI. CL Brener, the reference strain of the  T. cruzi  genome project, is a hybrid with a genome assembled into 41 putative chromosomes. Gene copy number variation (CNV) is well documented as an important mechanism to enhance gene expression and variability in  T. cruzi . Chromosomal CNV (CCNV) is another level of gene CNV in which whole blocks of genes are expanded simultaneously. Although the  T. cruzi  karyotype is not well defined, several studies have demonstrated a significant variation in the size and content of chromosomes between different  T. cruzi  strains. Despite these studies, the extent of diversity in CCNV among  T. cruzi  strains based on a read depth coverage analysis has not been determined.    Results  We identify the CCNV in  T. cruzi  strains from the TcI, TcII and TcIII DTUs, by analyzing the depth coverage of short reads from these strains using the 41 CL Brener chromosomes as reference. This study led to the identification of a broader extent of CCNV in  T. cruzi  than was previously speculated. The TcI DTU strains have very few aneuploidies, while the strains from TcII and TcIII DTUs present a high degree of chromosomal expansions. Chromosome 31, which is the only chromosome that is supernumerary in all six  T. cruzi  samples evaluated in this study, is enriched with genes related to glycosylation pathways, highlighting the importance of glycosylation to parasite survival.    Conclusions  Increased gene copy number due to chromosome amplification may contribute to alterations in gene expression, which represents a strategy that may be crucial for parasites that mainly depend on post-transcriptional mechanisms to control gene expression.    Electronic supplementary material  The online version of this article (doi:10.1186/s12864-015-1680-4) contains supplementary material, which is available to authorized users.

Chromosomal copy number variation reveals differential levels of genomic plasticity in distinct Trypanosoma cruzi strains