Repeat-Driven Generation of Antigenic Diversity in a Major Human Pathogen, Trypanosoma cruzi

Abstract

Trypanosoma cruzi, a zoonotic kinetoplastid protozoan parasite, is the causative agent of American trypanosomiasis (Chagas disease). Having a very plastic, repetitive and complex genome, the parasite displays a highly diverse repertoire of surface molecules, with pivotal roles in cell invasion, immune evasion and pathogenesis. Before 2016, the complexity of the genomic regions containing these genes impaired the assembly of a genome at chromosomal level, making it impossible to study the structure and function of the several thousand repetitive genes encoding the surface molecules of the parasite. We here describe the genome assembly of the Sylvio X10/1 genome sequence, which since 2016 has been used as a reference genome sequence for T. cruzi clade I (TcI), produced using high coverage PacBio single-molecule sequencing. It was used to analyze deep Illumina sequence data from 34 T. cruzi TcI isolates and clones from different geographic locations, sample sources and clinical outcomes. Resolution of the surface molecule gene distribution showed the unusual duality in the organization of the parasite genome, a synteny of the core genomic region with related protozoa flanked by unique and highly plastic multigene family clusters encoding surface antigens. The presence of abundant interspersed retrotransposons in these multigene family clusters suggests that these elements are involved in a recombination mechanism for the generation of antigenic variation and evasion of the host immune response on these TcI strains. The comparative genomic analysis of the cohort of TcI strains revealed multiple cases of such recombination events involving surface molecule genes and has provided new insights into T. cruzi population structure.

The gene repertoire of the main cysteine protease of Trypanosoma cruzi, cruzipain, reveals four sub-types with distinct active sites

“…Artificial truncated cruzipain genes could be a consequence of assembly limitations imposed by repetitive sequences including multigene families such as cruzipains, a largely recognized challenge faced during T. cruzi genome assembly (revised by 33 ). Another possibility related to the biology of the parasite is that truncated sequences could be the result of recombination events, a known mechanism to generate sequence variability in T. cruzi multigene families, but that may also generate pseudogenes 34 , 35 . Gene conversion is also a possibility, considering their homology and the short distances between copies in a cluster, and could have contributed both to the expansion of the family and to the generation of variability.…”

The gene repertoire of the main cysteine protease of Trypanosoma cruzi, cruzipain, reveals four sub-types with distinct active sites

“…Arti cial truncated cruzipain genes could be a consequence of assembly limitations imposed by repetitive sequences including multigene families such as cruzipains, a largely recognized challenge faced during T. cruzi genome assembly (revised by 33 ). Another possibility related to the biology of the parasite is that truncated sequences could be the result of recombination events, a known mechanism to generate sequence variability in T. cruzi multigene families, but that may also generate pseudogenes 34,35 . Gene conversion is also a possibility, considering their high homology and the short distances between copies in a cluster, and could have contributed both to the expansion of the family and to the generation of variability.…”

Optimization of DNA Extraction from Field-Collected Mammalian Whole Blood on Filter Paper for Trypanosoma cruzi (Chagas Disease) Detection

“…T . cruzi parasites used for spiking were the Vero cell culture supernatants of the parasite strain TD25 isolated from a triatomine collected in Texas [ 31 ].…”