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

Autor: de Paula Baptista R; Houston Methodist Research Institute, Houston, TX, 77030, USA.; Department of Medicine, Weill Cornell Medicine College, New York, NY, 10065, USA., Tucker MS; Animal Parasitic Diseases Laboratory, Agricultural Research Service, US Department of Agriculture, Beltsville, MD, 20705, USA., Valente MJ; Animal Parasitic Diseases Laboratory, Agricultural Research Service, US Department of Agriculture, Beltsville, MD, 20705, USA., Srivastava SK; Animal Parasitic Diseases Laboratory, Agricultural Research Service, US Department of Agriculture, Beltsville, MD, 20705, USA., Chehab N; Animal Parasitic Diseases Laboratory, Agricultural Research Service, US Department of Agriculture, Beltsville, MD, 20705, USA., Li A; Animal Parasitic Diseases Laboratory, Agricultural Research Service, US Department of Agriculture, Beltsville, MD, 20705, USA., Shaik JS; Insights and Analytics, Applied Data Science and Learning, Data Science Institute, Takeda, Cambridge, MA, 02142, USA., Ramirez JD; Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia.; Molecular Microbiology Laboratory, Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA., Rosenthal BM; Animal Parasitic Diseases Laboratory, Agricultural Research Service, US Department of Agriculture, Beltsville, MD, 20705, USA., Khan A; Animal Parasitic Diseases Laboratory, Agricultural Research Service, US Department of Agriculture, Beltsville, MD, 20705, USA. asis.khan@usda.gov.
Jazyk: angličtina
Zdroj: Scientific reports [Sci Rep] 2024 Jun 12; Vol. 14 (1), pp. 13582. Date of Electronic Publication: 2024 Jun 12.
DOI: 10.1038/s41598-024-63783-5
Abstrakt: 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.
(© 2024. This is a U.S. Government work and not under copyright protection in the US; foreign copyright protection may apply.)
Databáze: MEDLINE
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