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April 1st, 2025
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Institut Pasteur de Montevideo
genomics
biorxiv

Trypanosoma cruzi Has 32 Chromosomes: A Telomere-to-Telomere Assembly Defines Its Karyotype.

Greif, G.Open in Google Scholar•Diaz-Viraque, F.Open in Google Scholar•Chiribao, M. L.Open in Google Scholar•Sanz-Rodriguez, C.Open in Google Scholar•Robello, C.Open in Google Scholar

Trypanosoma cruzi, the causative agent of Chagas disease, exhibits remarkable genomic plasticity and possesses an expanded genome rich in multigene families. However, its precise chromosomal composition has remained elusive due to challenges in resolving repetitive regions. Using PacBio HiFi long-read sequencing, we assembled the complete nuclear genome of the Dm28c strain into 32 telomere-to-telomere chromosomes. The assembly revealed conserved chromosomal structures and synteny patterns when compared to the independently sequenced Dm25 strain, both of which belong to clade A (TcI). This indicates that the 32-chromosome karyotype is a stable and conserved feature of T. cruzi. Through a comprehensive annotation pipeline, we refined gene content and resolved haplotypes, resulting in an approximately 25% reduction in core gene redundancy. All chromosomes demonstrate a conserved compartmentalized architecture consisting of core, disruptive, and newly characterized subtelomeric regions. Subtelomeres, enriched in RHS, TS, and DGF-1 genes but lacking MASP and mucins, create a distinct third genomic compartment. Telomere analysis showed significant length heterogeneity, which may influence subtelomeric gene regulation. Overall, this work defines the complete chromosomal complement of T. cruzi, establishing a solid framework for comparative genomics and enabling detailed studies into genome organization, antigenic variability, and evolutionary dynamics across strains and clades. This assembly redefines the genomic reference landscape, paving the way for future research on T. cruzi fundamental biology, pathogenic diversity, and adaptive mechanisms.

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