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Sequencing Suggests Intestinal Parasite May Be Two Species

NEW YORK (GenomeWeb News) – The Giardia intestinalis parasite behind the human intestinal disease giardiasis may actually be two species, according to a paper appearing online today in PLoS Pathogens on the draft genome sequence of a G. intestinalis strain from the assemblage B genotype.

The team used Roche 454 sequencing to sequence the genome of a G. intestinalis isolate called GS, which belongs to the "B" G. intestinalis genotype. When they compared the GS draft genome to that of an isolate called WB from the "A" genotype, the researchers discovered a slew of differences between the two isolates.

"The genomic differences between WB and GS may explain some of the observed biological and clinical differences between the two isolates, and it suggests that assemblage A and B Giardia can be two different species," senior author Staffan Svard, a cell and molecular biology researcher at Uppsala University, and his co-authors wrote.

Giardiasis is a diarrheal disease caused by Giardia — a single-celled protozoan that contains a tetrapolid genome housed in two diploid nuclei. It affects roughly two to seven percent of people in developed countries and as many as 30 percent of people in developing countries.

Although seven G. intestinalis genotypes or assemblages have been identified so far, the authors noted, just two — assemblages A and B — have been linked to human infections. Past studies have uncovered genetic differences between these two genotypes, though whole-genome sequence for G. intestinalis (also known as G. lamblia or G. duodenalis) has only been available recently.

In 2007, American, Swiss, and Swedish researchers sequenced the 11.7 million base pair genome of an assemblage A parasite called WB. For the latest paper, Svard and his colleagues tackled the genome of an assemblage B G. intestinalis isolate called GS using a Roche Genome Sequencer FLX.

After sequencing a draft version of the GS genome to about 16 times coverage, the team analyzed and compared this genome with that of the assemblage A isolate sequenced previously. The researchers noted that there are still many gaps in the GS draft genome — mainly due to the preponderance of repeats in the genome.

The researchers identified 4,470 intact and 221 interrupted apparent protein-coding genes, 124 small RNA genes, and 69 transfer RNAs in the GS genome.

Their results suggest about 77 percent nucleotide identity between the two Giardia isolates sequenced so far — and similar levels of amino acid identity. The researchers noted that the newly sequenced assemblage B genome contains 28 protein coding genes not present in the assemblage A, WB genome but is missing at least three WB protein coding genes.

When the researchers compared the allelic sequence variation in regions of the WB and GS genomes for which at least ten times sequence coverage was available, they found that the new GS genome from assemblage B contained far more polymorphisms than the assemblage A genome.

Based on these results, the team speculated that there may be differences between gene sequences found in the two nuclei of GS cells. They also noted that some genes showed more allelic variation than others.

The team's subsequent analyses also provided new insights into everything from messenger RNA introns and splicing patterns to protein families and functions present in the GS isolate. For instance, the researchers found evidence that some proteins overlap with — and may have originated in — bacteria.

Overall, the researchers argued that there are enough genetic differences between the two Giardia isolates to consider them distinct — at least by some species definitions. Still, they noted that the sequences of additional assemblage A and B isolates will have to be evaluated before drawing conclusions about the relationships between the genotypes as a whole.

"The WB and GS isolates can be considered as separate species according to the phylogenetic species concept because they group into different assemblages in genotyping studies and our data show an extensive primary sequence divergence across the majority of the genes," they wrote. "However, not enough data is available to define them as separate species according to many of the other species concepts."

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