Background: The diarrhea-causing protozoan Giardia intestinalis makes up a species complex of eight different assemblages (A-H), where assemblage A and B infect humans. We have performed whole genome sequencing of two sub-assemblage AII isolates, recently axenized from symptomatic patients, to study the genetic diversity within assemblage A and to identify new assemblage A-specific genotyping targets.
Results: Several biological differences between the assemblage A isolates were identified, including a difference in growth medium preference. The two AII isolates were of different sub-assemblage types (AII-1 (AS98) and AII-2 (AS175)) and showed size differences in the smallest chromosomes. The amount of genetic diversity was characterized in relation to the genome of an assemblage AI isolate (WB). Our analyses indicate that the divergence between AI and AII is approximately 1%, represented by ~100,000 single nucleotide polymorphisms (SNP). Moreover, SNPs are homogeneously distributed over the chromosomes with an enrichment in regions containing surface antigens and non-coding sequences. The level of allelic sequence heterozygosity (ASH) in the two AII isolates were found to be 0.25-0.35%, which is 25-30-fold higher than in the WB isolate. 37 proteinencoding genes, not found in the WB genome, were identified in the two AII genomes. The large gene families of variant-specific surface proteins (VSPs) and high cysteine membrane proteins (HCMPs) showed isolatespecific divergences of the gene repertoires. Certain genes, often in small gene families with 2 to 7 members, showed high sequence diversity between the assemblage A isolates and they could have important roles in hostparasite interactions. A subset of the variable genes was used to develop new genotyping methods for assemblage A isolates.
Conclusions: Our results show that there is a significant genomic variation in assemblage A isolates, in terms of chromosome size, gene content, surface protein repertoire and gene polymorphisms. This identified putative virulence genes and generated a new assemblage A-specific genotyping approach.