Tuesday, August 26, 2008

The Trichoplax Genome

 
Trichoplax adherens is a very simple animal that moves about on surfaces like a gigantic amoeba and ingests any food that it flows over. There are thought to be several species of Trichoplax in addition to Trichoplax adherens.

Because this is such a simple and unusual animal it has been assigned its own phylum, Placozoa with Trichoplax as the only genus.1

The diagram below is copied from Syed and Shierwater (2002). It shows clearly that Trichoplax adhaerens is a true metazoan with an upper (dorsal) epithelial layer, a lower (ventral) epithelial layer, and an internal layer of contractile fiber cells. There are at least four cell types, not counting the egg and sperm cells that have been reported by others.


Where does Trichoplax fit in the evolution of animals? Clearly, the lineage leading to modern Trichoplax must have diverged very early in animal evolution. This is why Trichoplax is often (incorrectly) referred to as a "primitive animal", or a "living fossil." (See Ryan Gregory's discussion of this terminology at: Kudos on the placozoan genome!.)

The exact branch point is hotly disputed. Did the ancestors of Trichoplax split off before or after the sponges (Porifera) or the Cnideria (jelleyfish, hydras, corals)? Is the modern form of Trichoplax the ancestral form or is it a derived and simplified version of a more complex animal?

video


The complete genome sequence of Trichoplax adherens has just been published in Nature (Srivastava et al. 2008). There's a pretty good press release on Bio News Net [Genome of simplest animal reveals ancient lineage, confounding array of complex capabilities]. In addition to Ryan Gregory's review, there's another by John Timmer at Nobel Intent (Ars Technica) [Sequencing the bizarre: the genome of a living fossil].

Trichoplax adherens has six chromosomes and a total genome size of about 98 × 106 base pairs (98 Mb). The authors identified 11,514 protein-encoding genes. Because the genome sequence is "only" 98% complete, it wasn't possible to reconstruct entire chromosomes and the association between the sequenced genome and particular chromosomes is impossible to establish due to the absence of genetic studies on Trichoplax (no linkage maps).

The genome is smaller than that of the green alga Chlamydomonas reinhardtii with a genome of 121 Mb and about 15,000 genes [The Genome of Chlamydomonas reinhardtii]. On the other hand, the Trichoplax genome is larger than that of other single-cell organisms such as the protist Giardia lamblia (12 Mb, ~6500 genes) [The Giardia lamblia Genome].

The Trichoplax genome is almost the same size as the C. elegans (nematode) genome at 97 Mb but C. elegans is thought to have more than 15,000 genes. Drosophila melanogaster at 180 Mb has ~16,000 genes and mammals have a genome of 3,300 Mb and 20,000 genes.

About 90% of the Trichoplax genes are present in other animals and the intron positions of the Trichoplax are mostly identical to those in other animals [Junk in Your Genome: Intron Size and Distribution]. This is powerful evidence that the phylum Placozoa belongs in the animal kingdom.

Srivastava et al. constructed a phylogenetic tree using 104 highly conserved genes from species whose complete genomes are available in the sequence databases. The tree (below) shows that the Trichoplax lineage branches after sponges (represented by Amphimedon queenslandica) but before cnidarians (Hydra magnipapillata). The result are not compatible with trees constructed using mitochondrial sequences or ribosomal RNA sequences but that's not too surprising. Mitochondrial DNA and ribosomal RNA sequences are often not reliable for this kind of work.


The conclusion is that Placozoa and most metazoans diverged about 600 million years ago but sponges diverged even earlier.


1. It isn't unusual to create separate phyla for organisms with distinct body plans but you wouldn't know that from the criticisms leveled at Stephen Jay Gould when he published Wonderful Life [Science and Philosophy Book Club: Wonderful Life]. Incidentally, in The Ancestor's Tale Dawkins readily accepts that Trichoplax adherens may be the sole species in the phylum Placozoa.

[Image Credit: The photograph of Trichoplax is from metamorphnet. That website also has some wonderful movies of Trichoplax.

Srivastava, M., Begovic, E., Chapman, J., Putnam, N.H., Hellsten, U., Kawashima, T., Kuo, A., Mitros, T., Salamov, A., Carpenter, M.L., Signorovitch, A.Y., Moreno, M.A., Kamm, K., Grimwood, J., Schmutz, J., Shapiro, H., Grigoriev, I.V., Buss, L.W., Schierwater, B., Dellaporta, S.L., Rokhsar, D.S. (2008) The Trichoplax genome and the nature of placozoans. Nature 454:955-960. [doi:10.1038/nature07191]

7 comments:

  1. This comment has been removed by the author.

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  2. "The result are not compatible with trees constructed using mitochondrial sequences or ribosomal RNA sequences but that's not too surprising. Mitochondrial DNA and ribosomal RNA sequences are often not reliable for this kind of work"

    I'd say that definitely there were morphological reasons to consider this basal, but otherwise there wasn't much morphological reason for a particular affinity to the eumetazoa. They could be the mos basal metazoa; also, the possiblity that placozoans are simplified sponges is not discarded by this new data, since porifera may be paraphyletic, including the clade placozoa+eumetazoa.

    Even genome wide-comparisons are likely to change if the taxon sampling is poor. Including intermediate forms can (and will!) change the structure of the tree.

    In this sense I commend the work for having included a choanoflagellate, but that's about it. The calcisponges are not there: only a demosponge. The deuterostome is..."human"! The protostomes are a snail and fruitfly, and both cnidarians are anthozoans (as far as I know). The ctenophores, as usual, are the elephant in the room: they usually have this thing: in molecular studies, they POOF! DISAPPEAR!!!

    There is no evident morphological signal. Placozoa are similar to some poriferan and cnidarian larvae, simpler if anything. It is usually the case that mithochondrial and ribosomal genes have better taxon sampling. I would take genes that have a good taxonomic sampling more seriously. We'll see what happens: There is still much "bizarre that needs sequencing!!!!

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  3. Hexactinlellid (silicatous)sponges, THOSE are the ones missing, crucial to this case (their spicules are the oldest in the fossil record)

    Despite the shortcomings of taxon sampling the genome-wide comparisons results are still a good possibility according to morphology and have basically confirming the morphologically most parsimonious assumption, that Placozoa are basal metazoa. Those aspects will for sure be maintained when taxon sampling is improved.

    The more specific questions may still find new answers with better data.

    BTW, of course, some sponges DO have fibrilar contractile cells; Actually the actin-myosin contractile apparatus is a pre-metacellular innovation.

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  4. It's a good post but has one flaw. The assumption "coding sequence = gene" is quite wrong. If a gene is the sequence responsible for a heritable trait, then there are a large number of RNAi genes that we know little about. Several, for example, are involved in malignancy, and that certainly is a heritable trait.

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  5. frank says,

    It's a good post but has one flaw. The assumption "coding sequence = gene" is quite wrong.

    I have never made that assumption as anyone who reads my opinions on genes and genomes would know.

    If a gene is the sequence responsible for a heritable trait, then there are a large number of RNAi genes that we know little about. Several, for example, are involved in malignancy, and that certainly is a heritable trait.

    I'm well aware of the existence of genes whose product is RNA. Been teaching that for over thirty years. We've known about small regulatory RNAs for almost as long.

    The question is not whether genes for small regulatory RNAs exist, it's whether there are a lot of them. I don't think there are lots of them, certainly not enough to make a significant difference in the number of genes.

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  6. I saw this on an ID website:

    http://www.thedesignmatrix.com/content/another-phylum-supports-front-loading/

    Could someone do a review of this website?

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  7. where can one get a copy of the video-clip on Trichoplax adhaerens for teaching purposes?
    Please reply to jco@helmholtz-hzi.de

    Very nice article
    John Collins

    ReplyDelete