The Giardia lamblia Genome

 
The sequence of the Giardia lamblia genome has just been published in this month's issue of Science [Morrison et al., 2007].

Giardia lamblia is a single-celled eukaryote with two nuclei and prominent flagella (undulipodia, cilia) [Giardia lamblia, Wikipedia]. In most classification schemes it is placed in the Diplomonadida group, which may or may not be accorded the rank of phylum [Giardia lamblia NCBI Taxonomy]. Giardia is an intestinal parasite that colonizes the small intestine causing diarrhea and sometimes pain and nausea.

Many of the press releases focus on the medical relevance of the work on Giardia but the direct quotations from the scientists involved in the project reveal the real purpose behind this genome sequencing project. For example, Mitchell Sogin is quoted in the Marine Biogical Laboratory press release [Giardia Genome Unlocked].

“We embarked upon this genome project because of its importance to human health and suggestions from earlier molecular analyses that Giardia represents a very early-diverging lineage in the evolutionary history of eukaryotes,” Sogin says. “Giardia’s genome content and architecture support these theories about the parasite’s ancestral character.”

Sogin has a long standing interest in the evolution of eukaryotes and I think it's fair to say that Giardiasis is not the main focus of his research at the Marine Biological Laboratory in Woods Hole, Maine Massachusetts (USA) .

The Giardia lamblia genome is ~11.7 Mb in size (11,700,00 base pairs). This makes it about the same size as the yeast genome and the largest bacterial genomes. Mammalian genomes are about 200-300 times larger.

Preliminary results indicate 6470 genes distributed on five chromosomes. Most of the genes do not have introns and the average distance between genes is a few hundred nucleotides. What this means is that the genome is very compact with hardly any junk DNA (77% of the genome corresponds to coding regions as opposed to less than 2% in humans).

The number of genes is similar to the number found in yeast [Saccharomyces Genome Database (SGD)]. Multicellular species have 15-25,000 genes.

The introduction to the Morrison et al. (2007) paper has a nice summary of the main problems with relating Giardia to other eukaryotes.

Unusual features of this enigmatic protist include the presence of two similar, transcriptionally active diploid nuclei and the absence of mitochondria and peroxisomes. Giardia is a member of the Diplomonadida, which includes both free-living (e.g., Trepomonas) and parasitic species. The phylogenetic position of diplomonads and related excavate taxa is perplexing. Ribosomal RNA (rRNA), vacuolar ATPase (adenosine triphosphatase), and elongation factor phylogenies identify Giardia as a basal eukaryote (2–4). Other gene trees position diplomonads as one of many eukaryotic lineages that diverged nearly simultaneously with the opisthokonts and plants. Discoveries of a mitochondrial-like cpn60 gene and a mitosome imply that the absence of respiring mitochondria in Giardia may reflect adaptation to a microaerophilic life-style rather than divergence before the endosymbiosis of the mitochondrial ancestor.

Originally, it was thought that Giardia must be part of a group that diverged very early on in eukaryotic evolution, before other lineages acquired mitochondria. However, in the past ten years or so these amitochondrial species have been shown to contain genes that are clearly derived from mitiochondria (e.g., cpn60, dnaK). Thus, it now appears that these species have lost their original mitochondria, calling into question their position at the root of the eukaryotic tree.

One of the main surprises is the confirmation of what had long been suspected: Giardia is missing some common eukaryotic genes. The title of the paper highlights this finding: "Genomic Minimalism in the Early Diverging Intestinal Parasite Giardia lamblia."

In many cases the protein machines in Giardia are simpler than those in other eukaryotes and some key metabolic enzymes are not present. Is this a derived phenomenon resulting from a parasitic lifestyle or is it indicative of a primitive state in eukaryotic evolution?

Morrison et al. (2007) indicate their preference ...

As discussed earlier, Giardia consistently shows a pattern of simplified molecular machinery, cytoskeletal structure, and metabolic pathways compared to later diverging lineages such as fungi and even Trichomonas or Entamoeba (Supporting Online Material; table S7 and fig. S5). A parsimonious explanation of this pattern is that Giardia never had many components of what may be considered "eukaryotic machinery," not that it had and lost them through genome reduction as is evident for Encephalitozoon. Taking a whole-evidence approach, one sees that these data reflect early divergence, not a derived genome.

They attempt to construct phylogenetic trees based on a number of newly sequenced genes but immediately encountered problems.

Phylogenetic inference alone cannot resolve Giardia's evolutionary history. Because so many of Giardia's genes may have been derived from horizontal transfer or be subject to accelerated evolution, only a subset can be used to infer phylogeny. Of the ~1500 genes for which there are known homologs, only a handful included diverse eukaryotic taxa and generated robust trees, largely because the sequences could not be unambiguously aligned. We generated and examined trees for many conserved proteins, and selected ribosomal proteins for a multigene data set because they are an ancient family, whose nature—interaction with rRNAs and with all cellular proteins during their synthesis—constrains their divergence.

Their data suggests that Giardia and its close relatives form a lineage that branches deeply in the eukaryotic tree suggesting that they diverged very early on in eukaryotic evolution (above, from the supplemental data). (Probably close to two billion years ago.)

In an article accompanying the original paper, Keeling (2007) discusses the implications. He includes the phylogenetic tree shown here [Deep Questions in the Tree of Life].

Eukaryotic evolution. The hypothetical evolutionary tree consists of five "supergroups" based on several kinds of evidence (15). The branching order of supergroups is unresolved, implying that the relationships are unknown rather than a simultaneous radiation. CM indicates the presence of cryptic mitochondria (hydrogenosomes or mitosomes). A question mark indicates that no organelle has yet been found.

This is not a consensus tree by any stretch. The existence of the five groups is hotly contested and it remains to be seen whether these groupings will gain widespread support. Notice that Keeling does not commit to a branching order for the five groups in spite of the conclusions of Morrison et al. (2007) in the paper he is reviewing.

What is clear is that the old trees based on ribosomal RNA genes are not reliable and other genes will have to be examined in future work. That's the real significance of the Giardia lamblia genome sequence and the sequences of the genomes of other simple eukaryotes. Given that Giardia is missing some important genes—posibly because of its parasitic lifestyle—this may not be an easy task. Keeling (2007) sums it up like this ....

The outcome of this debate affects not only our understanding of early eukaryotic evolution, but also our view of Giardia biology. Simple characteristics could be primitive or derived via reduction, alternatives with very different meanings. The simplicity of Giardia's molecular systems differs from that of known derived parasites (1, 13). However, different lineages can follow different reductive paths (14), so determining Giardia's origins independently of its simplicity is essential. Given the depth of these questions, the new life that Morrison et al. have breathed into the debates is welcome, and will ensure continued attention on both a fascinating cell and the origin of eukaryotes.

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[Photo Credits: The life cycle diagram is from the National Institutes of Health (USA) (Wikimedia Commons). The scanning electron micrograph of Giardia is from the Centers for Disease Control and Prevention (USA) (Wikimedia Commons)]

Morrison, H.G., McArthur, A.G., Gillin, F.D., Aley, S.B., et al. (2007) Genomic Minimalism in the Early Diverging Intestinal Parasite Giardia lamblia. Science 317:1921 - 1926. [Science]

Keeling, P.J. (2007) Deep Questions in the Tree of Life. Science 317:1875-1876. [Science]