show Abstracthide AbstractTrypanosoma cruzi is the causative agent of Chagas disease which affects millions of people primarily in Latin America. However, its genomic studies are greatly hampered by the lack of an acceptable reference genome. In order to regenerate a more suitable reference genome, two homozygous T. cruzi isolates, Brazil strain clone A4 (TcI) and Y strain clone C6 (TcII) were selected for Single-molecule, long-read sequencing platform (SMRT sequencing) to better resolve the genome complexity. Furthermore, Chicago and Dovetail Hi-C assays were performed to capture the chromosomal conformation of the parasite genome to obtain chromosome-level assemblies. Finally, annotation was manually curated for both genomes.