Comparative genomics of Giardia duodenalis sub-assemblage A1 beaver (Be-2) and human (WB-C6) strains show remarkable homozygosity, sequence similarity, and conservation of VSP genes

Authors: DE PAULA BAPTISTA, RODRIGO - Houston Methodist Research Institute; Tucker, Matthew; Valente, Matthew; SRIVASTAVA, SUBODH - Non ARS Employee; Chehab, Nadya; Li, Alison; RAMIREZ, JUAN - Universidad Del Rosario, Columbia; Rosenthal, Benjamin; Khan, Asis

Submitted to: Scientific Reports
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 6/3/2024
Publication Date: 6/12/2024
Citation: De Paula Baptista, R., Tucker, M.S., Valente, M., Srivastava, S., Chehab, N.L., Li, A.S., Ramirez, J., Rosenthal, B.M., Khan, A. 2024. Comparative genomics of Giardia duodenalis sub-assemblage A1 beaver (Be-2) and human (WB-C6) strains show remarkable homozygosity, sequence similarity, and conservation of VSP genes. Scientific Reports. 14(1). Article e13582. https://doi.org/10.1038/s41598-024-63783-5.
DOI: https://doi.org/10.1038/s41598-024-63783-5

Interpretive Summary: A billion cases of illness and millions of deaths take place every year globally due to zoonotic diseases. Strikingly, many foodborne outbreaks are linked to zoonotic pathogens, urging government intervention and public vigilance against the risks of catching foodborne diseases from farm-to-table dining. Most foodborne outbreaks are associated with diarrheal diseases caused by protozoan parasites such as Giardia. Although the combination of very few epidemiological studies using low-resolution genetic markers and highly fragmented whole genomes are all shedding light on Giardia research, still this field is in its infancy for molecular epidemiology and outbreak assessment. Well-assembled parasite genomes can aid efforts to identify genetic markers suitable for outbreak investigation and targets for intervention and management. Hence, USDA scientists generate a complete telomere-to-telomere draft genome of G. duodenalis without any gap using ultra-long sequence reads. Comparative analysis with previously published Giardia genome reveals a highly syntenic genome, and we correctly assembled a big missing piece into Chr4, which was misassembled in the previous reference genome. Comparative analysis also revealed a high degree of conservation in the ploidy, homozygosity, and the presence of cysteine-rich variant-specific surface proteins (VSPs) within the AI assemblage of Giardia. Hence, our work heralds a new era in the sequencing and assembly of genomes of Giardia, producing an assembly that should serve as a reference for efforts to understand host specificity, pathogenesis, drug development, and genome evolution.

Technical Abstract: Giardia duodenalis, a major cause of waterborne infection, infects a wide range of mammalian hosts and is subdivided into eight genetically well-defined assemblages named A through H. However, fragmented genomes and a lack of comparative analysis within and between the assemblages render unclear the molecular mechanisms controlling host specificity and differential disease outcomes. To address this, we generated a near-complete de novo genome of AI assemblage using the Oxford Nanopore platform by sequencing the Be-2 genome. We generated 148,144 long-reads with quality scores of'>'7. The final genome assembly consists of only nine contigs with an N50 of 3,045,186 bp. This assembly agrees closely with the assembly of another strain in the AI assemblage (WB-C6). However, a critical difference is that a region previously placed in the five-prime region of Chr5 belongs to Chr4 of Be-2. We find a high degree of conservation in the ploidy, homozygosity, and the presence of cysteine-rich variant-specific surface proteins (VSPs) within the AI assemblage. Our assembly provides a nearly complete genome of a member of the AI assemblage of G. duodenalis, aiding population genomic studies capable of elucidating Giardia transmission, host range, and pathogenicity.