title: The Giardia lamblia vsp gene repertoire: characteristics, genomic organization, and evolution.
abstract: BACKGROUND
  Giardia lamblia trophozoites colonize the intestines of susceptible mammals and cause diarrhea, which can be prolonged despite an intestinal immune response. The variable expression of the variant-specific surface protein (VSP) genes may contribute to this prolonged infection. Only one is expressed at a time, and switching expression from one gene to another occurs by an epigenetic mechanism.
  
  
  RESULTS
  The WB Giardia isolate has been sequenced at 10x coverage and assembled into 306 contigs as large as 870 kb in size. We have used this assembly to evaluate the genomic organization and evolution of the vsp repertoire. We have identified 228 complete and 75 partial vsp gene sequences for an estimated repertoire of 270 to 303, making up about 4% of the genome. The vsp gene diversity includes 30 genes containing tandem repeats, and 14 vsp pairs of identical genes present in either head to head or tail to tail configurations (designated as inverted pairs), where the two genes are separated by 2 to 4 kb of non-coding DNA. Interestingly, over half the total vsp repertoire is present in the form of linear gene arrays that can contain up to 10 vsp gene members. Lastly, evidence for recombination within and across minor clades of vsp genes is provided.
  
  
  CONCLUSIONS
  The data we present here is the first comprehensive analysis of the vsp gene family from the Genotype A1 WB isolate with an emphasis on vsp characterization, function, evolution and contributions to pathogenesis of this important pathogen.
authors.affiliation: Departments of Medicine and Immunobiology, University of Arizona College of Medicine, Tucson, AZ, USA. adamr@u.arizona.edu
authors.forename: Rodney D
authors.initials: RD
authors.lastname: Adam
authors.forename: Anuranjini
authors.initials: A
authors.lastname: Nigam
authors.forename: Vishwas
authors.initials: V
authors.lastname: Seshadri
authors.forename: Craig A
authors.initials: CA
authors.lastname: Martens
authors.forename: Gregory A
authors.initials: GA
authors.lastname: Farneth
authors.forename: Hilary G
authors.initials: HG
authors.lastname: Morrison
authors.forename: Theodore E
authors.initials: TE
authors.lastname: Nash
authors.forename: Stephen F
authors.initials: SF
authors.lastname: Porcella
authors.forename: Rima
authors.initials: R
authors.lastname: Patel
mesh_terms: D020816:Amino Acid Motifs; D000595:Amino Acid Sequence; D000953:Antigens, Protozoan / Q000737:chemistry / Q000235:genetics*; D017124:Conserved Sequence; D016054:DNA, Protozoan / Q000235:genetics; D019143:Evolution, Molecular; D018503:Genome, Protozoan / Q000235:genetics*; D023281:Genomics; D005838:Genotype; D016829:Giardia lamblia / Q000235:genetics*; D055029:Inverted Repeat Sequences / Q000235:genetics; D010802:Phylogeny; D017434:Protein Structure, Tertiary; D015800:Protozoan Proteins / Q000737:chemistry / Q000235:genetics*; D011544:Pseudogenes / Q000235:genetics; D011995:Recombination, Genetic; D016415:Sequence Alignment; D016615:Telomere / Q000235:genetics
chemical_list: D000953:Antigens, Protozoan; D016054:DNA, Protozoan; D015800:Protozoan Proteins; C072464:variant surface protein H7, Giardia lamblia