Histogram of pairwise nucleotide identities between orthologous genes. Histogram of pairwise nucleotide identities between orthologs of T. c. marinkellei B7 and T. c. cruzi CL Brener non-Esmeraldo-like haplotype. 5618 orthologs were included in the comparison, for which the average nucleotide identity was 92.6% ± 3.3 (Tcm vs Tcc CLBR non-Esm). The genes included in this analysis mainly comprised the non-repetitive component of these genomes. Orthologs were defined as the best reciprocal BLASTp hit between the genomes. Nucleotide sequences were aligned with ClustalW version 2.1. Mismatches (single nucleotide polymorphisms) within each alignment were identified and counted using a Perl script. Pairwise orthologs with lower identity than 80% were excluded from the analysis.