title: Identification of polymorphic genes for use in assemblage B genotyping assays through comparative genomics of multiple assemblage B Giardia duodenalis isolates.
abstract: Giardia duodenalis assemblage B is potentially a zoonotic parasite. The characterisation and investigation of isolates has been hampered by greater genetic diversity of assemblage B, limiting the application and utility of current genotyping loci. Since whole genome sequencing is the optimal high-throughput method for gene identification, the present study sequenced assemblage B isolate BAH15c1 and compared the sequence to the draft GS references to identify polymorphic genes for potential use in genotyping assays. The majority of the genome sequence was conserved between the two isolates, producing 508 contigs of 10.4 Mb with 4968 genes. Seventy polymorphic genes for potential use in genotyping assays were identified ranging in variation from elongation factor 1 α, which was the most conserved, through to triose phosphate isomerase, which was the most variable.
authors.affiliation: School of Veterinary and Life Sciences, Murdoch University, South Street, Murdoch,Western Australia, 6150, Australia. Electronic address: c.wielinga@murdoch.edu.au.
authors.forename: Caroline
authors.initials: C
authors.lastname: Wielinga
authors.affiliation: WHO Collaborating Centre for the Molecular Epidemiology of Parasitic Infections, School of Veterinary and Life Sciences, Murdoch University, South Street, Murdoch, Western Australia, 6150, Australia.
authors.forename: R C Andrew
authors.initials: RCA
authors.lastname: Thompson
authors.affiliation: South Australian Water Corporation Adelaide, SA 5000, Australia.
authors.forename: Paul
authors.initials: P
authors.lastname: Monis
authors.affiliation: School of Veterinary and Life Sciences, Murdoch University, South Street, Murdoch,Western Australia, 6150, Australia.
authors.forename: Una
authors.initials: U
authors.lastname: Ryan
mesh_terms: D016000:Cluster Analysis; D016054:DNA, Protozoan / Q000737:chemistry / Q000235:genetics*; D017125:Genes, Protozoan; D005838:Genotype; D060005:Genotyping Techniques / Q000379:methods*; D016829:Giardia lamblia / Q000145:classification* / Q000235:genetics*; D008969:Molecular Sequence Data; D011110:Polymorphism, Genetic; D017422:Sequence Analysis, DNA
chemical_list: D016054:DNA, Protozoan
keywords: Annotation; Assemblage B; Assembly; Genome; Genotyping; Giardia