Genome analysis and comparative genomics of a Giardia intestinalis assemblage E isolate

Abstract

BackgroundGiardia intestinalis is a protozoan parasite that causes diarrhea in a wide range of mammalian species. To further understand the genetic diversity between the Giardia intestinalis species, we have performed genome sequencing and analysis of a wild-type Giardia intestinalis sample from the assemblage E group, isolated from a pig.ResultsWe identified 5012 protein coding genes, the majority of which are conserved compared to the previously sequenced genomes of the WB and GS strains in terms of microsynteny and sequence identity. Despite this, there is an unexpectedly large number of chromosomal rearrangements and several smaller structural changes that are present in all chromosomes. Novel members of the VSP, NEK Kinase and HCMP gene families were identified, which may reveal possible mechanisms for host specificity and new avenues for antigenic variation. We used comparative genomics of the three diverse Giardia intestinalis isolates P15, GS and WB to define a core proteome for this species complex and to identify lineage-specific genes. Extensive analyses of polymorphisms in the core proteome of Giardia revealed differential rates of divergence among cellular processes.ConclusionsOur results indicate that despite a well conserved core of genes there is significant genome variation between Giardia isolates, both in terms of gene content, gene polymorphisms, structural chromosomal variations and surface molecule repertoires. This study improves the annotation of the Giardia genomes and enables the identification of functionally important variation.

Giardia duodenalisAssemblage-Specific Induction of Apoptosis and Tight Junction Disruption in Human Intestinal Epithelial Cells: Effects of Mixed Infections

“…Here, we demonstrate that these effects are not only isolate specific but also assemblage specific. Indeed, most severe abnormalities after infection with single isolates were observed in epithelia exposed to BAH12c14, a clone with mixed assemblage A and B genotypic characteristics, or in those epithelial monolayers exposed to assemblage E, a genotype believed to infect livestock but not humans (Monis et al, 2009;Jerlstr¨om-Hultqvist et al, 2010). Interestingly, the mono-infection with assemblage E (known to infect livestock) induced more-severe ZO-1 disruptions and apoptosis in the human HCT-8 epithelia than did monoinfections with representatives of human-specific assemblages A or B.…”

Stable Transfection of the Diplomonad Parasite Spironucleus salmonicida

“…The excavate order Diplomonadida belongs to an undersampled part of eukaryotic diversity, and studies performed so far have indicated substantial diversity within the order, including alternative genetic codes (21), differences in the number of nuclei, and large genomic differences between morphologically similar organisms (2,7,15,30).…”

“…However, to date, there are only two diplomonads for which transfection systems have been constructed. Giardia intestinalis was the first transfected diplomonad (32), and it is by far the most-studied organism, benefiting from the wealth of genomic information that is available (7,15,24). Spironucleus vortens, the likely cause of the "hole-in-the-head" disease in tropical fish species (26), has been successfully transfected and has many favorable characteristics as a model organism, such as wide temperature tolerance and extremely rapid growth in vitro to high cell densities (6,23,31).…”

Nuclear Inheritance and Genetic Exchange without Meiosis in the Binucleate ParasiteGiardia intestinalis

“…To date, the genomes of three Giardia assemblages (genotypes) have been sequenced. Two of these, assemblages A and E, contain extremely low levels of allelic heterozygosity -less than 0.01% (Morrison et al, 2007;Jerlström-Hultqvist et al, 2010). These results are surprising because, in a presumed asexual organism with two independent nuclei, the nuclear genomesand perhaps even homologous chromosomes -would be expected to diverge over time owing to genetic drift (Birky, 2010).…”

“…1C,D). The genomes of most Giardia isolates contain very low levels of heterozygosity (Morrison et al, 2007;Teodorovic et al, 2007;Lasek-Nesselquist et al, 2009;Jerlström-Hultqvist et al, 2010), suggesting that the two nuclear genomes are able to exchange genetic information during the Giardia life cycle. The Giardia genome also contains seven homologs of meiosis-specific genes: Spo11, Hop1, Dmc1a, Dmc1b, Hop2, Mnd1 and Mer3 (Ramesh et al, 2005;Malik et al, 2008), which in most organisms are expressed only during meiosis and are specifically involved in meiotic homologous recombination.…”