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

Rodrigo de Paula Baptista, Matthew S. Tucker, Matthew J. Valente, Subodh K. Srivastava, Nadya Chehab, Alison Li, Jahangheer S. Shaik, Juan David Ramirez, Benjamin M. Rosenthal, Asis Khan

Research output: Contribution to journalArticlepeer-review

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.

Original languageEnglish (US)
Article number13582
JournalScientific Reports
Volume14
Issue number1
DOIs
StatePublished - Dec 2024

Keywords

  • Annotation
  • Genome assembly
  • Giardia
  • Long-read sequencing
  • Ploidy
  • Synteny

ASJC Scopus subject areas

  • General

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