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Friday, July 6, 2007

Cnidarian Double Whammy: Anemone Genome Completed and a Worm Thats a Jelly!

Its been a long time in the making and I know everyone is as excited as I am that the first cnidarian genome is finished! This is monumental for cnidarian biologists (such as I sometimes fancy myself to be). The lucky species is Nematostella vectensis (its pimp name is the starlet sea anemone),a small edwardsiid anemone quickly becoming a model organism in developmental biology and now comparative genomics.

Curiously, the genome more closely resembles that of the human and other vertebrate genomes rather than invertebrate genomes such as other model organisms Drosophila (Arthropoda) and C. elegans (Nematoda). Nicholas Putnam, lead author of the study elaborates that this surprising result may be due to greater retention of ancestral genes in the anemones and vertebrates, whereas these tend to be lost at higher rates in Drosophila and C. elegans.

"In many ways, the ancestral genome was not so different from ours; it was intron-rich and contained nearly complete toolkits for animal biochemistry and development,which can now be recognized as pan-eumetazoan, as well as the core gene set required to execute sophisticated neural and muscular function. The ancestor had blocks of linked genes that remain together in the modern human and anemone genomes—the oldest known conserved synteny outside of prokaryotic operons. Whereas fruit flies and soil nematodes have proven to be exquisite model systems for dissecting the genetic underpinnings of metazoan development and physiology, their genomes are relatively poor models for the ancestral eumetazoan genome, having lost introns, genes, and gene linkages."-Putnam et al. 2007. Science 317: 86-94

The sea anemone genome is estimated to contain about 18,000 genes compared to a reasonable estimate for the human genome at around 20,000 genes. These 18k genes are spread over 30 chromosomes. Furthermore, over 80% of the anemone's introns are in the same place as human's!
"Only 20 percent of the ancestral eumetazoan genes seem to be unique to animals. Fifteen percent of these seem to be completely novel - we can't identify any related gene in non-animals. The other five percent were formed through substantial modifications to very ancient genes."-Study co-author Daniel Rokhsar, quoted from UC-Berkeley press release on ScienceDaily.
“Nematostella’s genome may provide more insights into the functional evolution of human genes than many far more closely related animals.”-Co-author John Finnerty, quoted in Pennisi 2007. Science 317: 27, confirming the superiority of the sea anemone to all other phyla in being able to answer "What is the meaning life?" I know there is an anemone out there with 42 chromosomes...

This is fantastic start that will undoubtedly open many interesting doors in comparative genomics. I will be anxiously awaiting more results, especially in understanding the origin of novel genes to the animal kingdom relative to other eukaryotic kingdoms (Plantae and Fungi). The next genome? After reading the latest on Zooillogix today, it is definitely got to be Buddenbrockia plumatellae. It looks like a worm, but is completely symmetrical in cross-section. In the words of Peter Holland:
"It has no mouth, no gut, no brain and no nerve cord. It doesn’t have a left or right side or a top or bottom – we can’t even tell which end is the front!" (quoted from Physorg)

This study was also published in the latest issue of Science (way to bump up the invert presence!) and answers the paradox, what the $@#! is this thing?! Analysis of 50 genes (thats 31,092 amino acid alignments) confirms that 97% of the time Buddebrockia plumatellae clusters with medusozoan cnidarians. I would say that is pretty good evidence. The authors conclude that
"This active muscular worm increases the known diversity in cnidarian body plans and demonstrates that a muscular, wormlike form can evolve in the absence of overt bilateral symmetry."
Is that funding bells I hear ringing? This is an amazing evolutionary question on how body form is controlled at the genetic level. Let me clear things up a bit. Buddebrockia is a myxozoan. A strange group of typically amoeboid parasites, with Buddenbrockia being a parasite of bryozoans (see picture below of new cnidarian exiting a bryozoan zooid). Myxozoans have strange nematocyst-looking cells called polar capsules. Some consider them reduced cnidarians, though with the discovery of the worm-like Buddenbrockia plumatellae and some Hox genes support a bilateria origin. Confused or just weirded out? Hopefully this study lays to rest of some of this conundrum. Although, it opens up infinitely more conundrums. Such as, if these are really cnidarians, albeit highly derived parasitic forms, how can there be this amazing diversity of body form from medusoid, polypoid, amoeboid, worm-like, and planular larvae all within a single phylum. I remind you that the Cnidaria are a well-supported clade!

Photo credit: Sylvie Tops


  1. Very nice post. I know this is a bit of a tangent, but did the paper discuss (or do you have any thoughts on) the evolutionary implication/cause of the lost features in the fruit fly and soil nematode genomes?

    Is it simply evolution by accident?

  2. They did not go into this detail but to talk about intron loss/gain. I suspect that will be paper coming out in the near future. From the article, it shows that intron loss is much greater in nematode and fly, intermediate in sea squirt and low in human and anemone. I don't know if anyone has ever studied the relationship between intron loss and evolutionary specialization. It seems like an interesting question to me. Insects are exceptionally adept at specialization. The nematodes small size, makes becoming reproductively isolated easier and their simple body plan might allow them to specialize easily as well. Both insects and nematodes are pretty species-rich taxa as well compared to vertebrates and urochordates. I would suspect that cnidarian species diversity is more or less intermediate between the two.

    I don't believe "evolution by accident" explains the great intron loss in fly and nematode relative to the other taxa analysed. We are looking at 70-90% loss. The authors also show that intron gains occur at a relatively constant rate across all the taxa examined.

    Thats my 2 cents anyways. I would love to hear more thoughts about this!

  3. I was really curious about the Buddebrockia paper, and was a little dissapointed that, at least in an opening fluff piece, no one discussed the profound evolutionary implications. I'm a big fan of the Cnidarian planula->Acoel theory myself, from a storytelling perspective, but does this new analysis give us another evolutionary halfway house?

    Oh, and, 'alo there from BML!

  4. Hello Mr. Byrnes (or is Dr. Byrnes by now??). I agree about the Buddenbrockia paper. Although, it open up another cool story. That myxozoans are are a highly derived branch on the cnidarian tree. Therefore the cnidarian bauplan is flexible enough, genetically, to allow for more than type of symmetry. It is interesting to me how this got fixed in the bilateria.

    The planula->acoel theory is a certainly nice story. Bagunà & Riutort 2004 erected a new phylum, Acoelmorpha, to accomodate the Acoela and Nemertodermatida based on molecular and morphological characters. This new "phylum" is basal to the platyhelminthes and hence intermediate between the Diploblastica (Cnidaria + Ctenophora + Porifera - although i don't agree with the authors of including Porifera with diploblast...).

    So whether Buddenbrockia or other myxozoans are another step connecting cnidarians to acoels would be a great hypothesis to test. I would include members of all 4 classes of cnidaria, ctenophora, platyhelminthes, acoela, porifera as the outgroup and a lophophorate, protostome and deuterstome for good measure. All the sequences should now be in genbank, so this could be a simple hypothesis to test! If I only the time... hmm... maybe I can squeeze it in. Although I'm sure other people recognize this as the next step too...

    Great to hear from the BML, keep checking back often. I love I'm a Chordata, Urochordata blog btw! Just the title cracks me up.

  5. Kevin,

    Sorry for not getting back sooner. Thanks for the thoughtful reply. Speciation is only one potential implication. I guess I was thinking more about things like the role introns and gene rearrangements play in the evolution of novel gene function or activation of pseudogenes.

  6. Andrew,
    As partly a systematicist (the other part ecologist i guess), I tend to think in terms of speciation. Molecular evolution is something I am getting more into right now preparing for my comps.

    I don't know if anyone has ever correlated diversity within a taxon to the amount of gene rearrangements and introns. Mammals and anemones are not particularly diverse taxa with regards to insects and nematodes. Yet both insects and nematodes have lost more introns and have fewer gene rearrangements. So the hypothesis to test then becomes taxonomic diversity (i.e. number of species) predicts amount of introns and/or amount of gene duplications. This is interesting to me because it links morphological classification with molecular evolution. This is why I believe every new species should be described based on morphology but put in context of evolution using gene trees.

    Of course I am going off on a tangent because you asked me about evolution of novel gene function and activation of pseudogenes. This is an area I must admit I don't know a whole lot about. Maybe RPM at Evolgen will read this and weigh in. Gene rearrangement can certainly result in novel gene function. It might also result in regulating genes in a new way or shutting off important genes downstream.

    Going on a far off limb, but perhaps with the Buddenbrockia paper I also talked about, the evolution of the Myxozoa may have been from developmental gene rearrangements resulting in the body form present today. And continuing with the Acoel theory from my previous comment, Some researchers hypothesize that the acoel was a planula that never metamorphosed. I guess losing all remnants of nematocysts.

    What do you, or anyone else, think?


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