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Background   Trypanosoma conorhini  and  Trypanosoma rangeli , like  Trypanosoma cruzi,  are kinetoplastid protist parasites of mammals displaying divergent hosts, geographic ranges and lifestyles. Largely nonpathogenic  T. rangeli  and  T. conorhini  represent clades that are phylogenetically closely related to the  T. cruzi  and  T. cruzi -like taxa and provide insights into the evolution of pathogenicity in those parasites.  T. rangeli , like  T. cruzi  is endemic in many Latin American countries, whereas  T. conorhini  is tropicopolitan.  T. rangeli  and  T. conorhini  are exclusively extracellular, while  T. cruzi  has an intracellular stage in the mammalian host.    Results  Here we provide the first comprehensive sequence analysis of  T. rangeli  AM80 and  T. conorhini  025E, and provide a comparison of their genomes to those of  T. cruzi  G and  T. cruzi  CL, respectively members of  T. cruzi  lineages TcI and TcVI. We report de novo assembled genome sequences of the low-virulent  T. cruzi  G,  T. rangeli  AM80, and  T. conorhini  025E ranging from ~ 21–25 Mbp, with ~ 10,000 to 13,000 genes, and for the highly virulent and hybrid  T. cruzi  CL we present a ~ 65 Mbp in-house assembled haplotyped genome with ~ 12,500 genes per haplotype. Single copy orthologs of the two  T. cruzi  strains exhibited ~ 97% amino acid identity, and ~ 78% identity to proteins of  T. rangeli  or  T. conorhini . Proteins of the latter two organisms exhibited ~ 84% identity.  T. cruzi  CL exhibited the highest heterozygosity.  T. rangeli  and  T. conorhini  displayed greater metabolic capabilities for utilization of complex carbohydrates, and contained fewer retrotransposons and multigene family copies, i.e. trans-sialidases, mucins, DGF-1, and MASP, compared to  T. cruzi .    Conclusions  Our analyses of the  T. rangeli  and  T. conorhini  genomes closely reflected their phylogenetic proximity to the  T. cruzi  clade, and were largely consistent with their divergent life cycles. Our results provide a greater context for understanding the life cycles, host range expansion, immunity evasion, and pathogenesis of these trypanosomatids.    Electronic supplementary material  The online version of this article (10.1186/s12864-018-5112-0) contains supplementary material, which is available to authorized users.

Genomic comparison of Trypanosoma conorhini and Trypanosoma rangeli to Trypanosoma cruzi strains of high and low virulence