Journal Article

Whole genome sequencing of Trypanosoma cruzi field isolates reveals extensive genomic variability and complex aneuploidy patterns within TcII DTU

de Almeida, Laila Viana, Dias, Fernando Hugo Cunha, Galvão, Lúcia M. C., Bartholomeu, Daniella C., Reis-Cunha, João Luís, Coqueiro-dos-Santos, Anderson, D’Ávila, Daniella Alchaar, Cardoso, Mariana Santos, Baptista, Rodrigo P., Rodrigues-Luiz, Gabriela F., Valdivia, Hugo O., Chiari, Egler, Cerqueira, Gustavo Coutinho, Fujiwara, Ricardo Toshio

2018

Overview

Background Trypanosoma cruzi , the etiologic agent of Chagas disease, is currently divided into six discrete typing units (DTUs), named TcI-TcVI. TcII is among the major DTUs enrolled in human infections in South America southern cone, where it is associated with severe cardiac and digestive symptoms. Despite the importance of TcII in Chagas disease epidemiology and pathology, so far, no genome-wide comparisons of the mitochondrial and nuclear genomes of TcII field isolates have been performed to track the variability and evolution of this DTU in endemic regions. Results In the present work, we have sequenced and compared the whole nuclear and mitochondrial genomes of seven TcII strains isolated from chagasic patients from the central and northeastern regions of Minas Gerais, Brazil, revealing an extensive genetic variability within this DTU. A comparison of the phylogeny based on the nuclear or mitochondrial genomes revealed that the majority of branches were shared by both sequences. The subtle divergences in the branches are probably consequence of mitochondrial introgression events between TcII strains. Two T. cruzi strains isolated from patients living in the central region of Minas Gerais, S15 and S162a, were clustered in the nuclear and mitochondrial phylogeny analysis. These two strains were isolated from the other five by the Espinhaço Mountains, a geographic barrier that could have restricted the traffic of insect vectors during T. cruzi evolution in the Minas Gerais state. Finally, the presence of aneuploidies was evaluated, revealing that all seven TcII strains have a different pattern of chromosomal duplication/loss. Conclusions Analysis of genomic variability and aneuploidies suggests that there is significant genomic variability within Minas Gerais TcII strains, which could be exploited by the parasite to allow rapid selection of favorable phenotypes. Also, the aneuploidy patterns vary among T. cruzi strains and does not correlate with the nuclear phylogeny, suggesting that chromosomal duplication/loss are recent and frequent events in the parasite evolution.

• Publisher: BioMed Central,BioMed Central Ltd,Springer Nature B.V,BMC
• Subject: Aneuploidy / Animal Genetics and Genomics / Animals / Bioinformatics / Biomedical and Life Sciences / Chagas disease / Chagas Disease - parasitology / Chagas Disease - transmission / Chromosomes / Copy number variation / DNA sequencing / DNA, Protozoan - genetics / Epidemiology / Etiology / Eukaryote microbial genomics / Evolution / Field isolates / Gene sequencing / Genetic aspects / Genetic variability / Genetic Variation / Genome, Protozoan / Genomes / Genomic variability / Genomics / Genotype / Humans / Infections / Insect Vectors - parasitology / Insects / Internet / Life Sciences / Microarrays / Microbial Genetics and Genomics / Mitochondria / Molecular Typing / Mountains / Multilocus sequence typing / Parasites / Patients / Phenotypes / Phylogenetics / Phylogeny / Plant Genetics and Genomics / Ploidy / Proteomics / Protozoa / Protozoan Proteins - genetics / Reproduction (copying) / Research Article / TcII / Trypanosoma cruzi / Trypanosoma cruzi - classification / Trypanosoma cruzi - genetics / Trypanosoma cruzi - isolation & purification / Vector-borne diseases / Vectors / Whole Genome Sequencing - methods