The sea urchin genome


Oh happy day, the Sea Urchin Genome Project has reached fruition with the publication of the full sequence in last week’s issue of Science. This news has been all over the web, I know, so I’m late in getting my two cents in, but hey, I had a busy weekend, and and I had to spend a fair amount of time actually reading the papers. They didn’t just publish one mega-paper, but they had a whole section on Strongylocentrotus purpuratus, with a genomics mega-paper and articles on ecology and paleogenomics and the immune system and the transcriptome, and even a big poster of highlights of sea urchin research (but strangely, very little on echinoderm development). It was a good soaking in echinodermiana.

I also browsed the web to see what was being reported about this landmark event. It was decidedly mixed. There were lots of decent summaries, but there were also two themes running through many of the headlines that I found annoying. First is exemplified by this: Decoded sea urchin genome shows surprising relationship to humans. That’s just wrong. One of the major rationales for sequencing the urchin genome was precisely because it is a non-chordate deuterostome—that is, it’s not a member of our phylum, but it is a member of a phylum that is one of the most closely related to ours. Perhaps “surprising” should be replaced with “expected”. Additionally, I don’t think the main interest here should be the animal’s similarity to us; what we have here is an example of a major lineage in metazoan evolution that stands on its own as a subject of great value.

Another trend that compounds the humancentric problem is the taint of biomedical speculation: Sea urchin genome could shed light on human disease, which you can also see in the print media. Here, the emphasis is on odd little factlets: they can live for over a century! They never get cancer! You, too, can someday hope to acquire the virtues of sessile or slow moving aquatic grazers and filter feeders! Again, these reports miss the real excitement of understanding a little more about a different organism.

So why should we care about the echinoderm genome? One reason is that we have well over a century of research on this organism, and it represents one of the key model systems in developmental biology. Every developmental biology instructor, when it comes time to explain the concept of regulation, probably starts with Driesch’s experiments, in which 4-cell echinoderm embryos were dissociated and subsequently developed into perfect, tiny, and complete larvae. Nowadays, they are still key players in understanding the molecular circuitry of developmental regulation.

Another reason is their position in metazoan phylogeny. Two major groups separated over half a billion years ago, the protostomes and deuterostomes. To understand the properties of the last common ancestor of the deuterostome line, we need to sample widely across the extant phyla in that clade, and limiting ourselves to just the vertebrates would give us a biased view. Would studying just mice, for instance, be sufficient to understand vertebrate diversity? Information about chordates, hemichordates, and echinoderms is necessary to get a clearer picture of the evolution of these groups, just as we need to know about both arthropods and molluscs to understand the protostomes, and we need all of them together to figure out the evolution of the Bilateria. And, of course, we need to widen our view to the fungi and plants and bacteria and protists to understand the evolution of life.

(click for larger image)

The phylogenetic position of the sea urchin relative to other model systems and humans. The chordates are shown on the darker blue background
overlapping the deuterostomes as a whole on a lighter blue background. Organisms for which genome projects have been initiated or finished are shown
across the top.

The echinoderms are a diverse and successful group, with a rich evolutionary history and many different extant forms. They’ve generally followed a very different ecological strategy than their cousins, the chordates, and so they represent an illustration of the degree of variation possible within the deuterostome plan. We want to learn how they achieve those differences.

Evolutionary history of the major echinoderm groups. Deuterostomia consists of three major groups: the chordates, hemichordates, and echinoderms, all with fossil representatives in the Cambrian. Cambrian echinoderms are recognized by the possession of stereom, but the phylogenetically most basal groups (such as stylophorans) lack the water vascular system, are highly asymmetrical, and possess gill slits. Pentameral symmetry is seen in two major Early Cambrian lineages, the edrioasteroids and eocrinoids; a third Early Cambrian taxon, the helicoplacoids, have an unusual threefold symmetry thought to be derived from the ancestral pentameral arrangement. All stem-group echinoderm lineages became extinct by the Carboniferous (indicated with crosses). Crown-group echinoderms, indicated by the yellow circle, consist of the five major extant lineages in addition to numerous extinct lineages not shown. Most class-level crown groups first appear in the latest Paleozoic-early Mesozoic, including echinoids. The lineage leading to echinoids, and hence to S. purpuratus, is indicated in purple. Known stratigraphic ranges are shown with thick lines, and inferred range extensions are shown with thin lines.

And look at them! They’re beautiful! They have ancestral similarities to chordates (check out the gill slits on the stylophorans), but they also have their own unique innovations, like the stereom and other aspects of their skeletons, and pentameral symmetry. What are the molecular correlates of those cool echinoderm specializations? Having the genome in hand is a tool to figure out the mechanisms behind those echinoderm specialties.

(click for larger image)

Stem-group (A to E) and crown-group (F to H) echinoderms. (A) The stylophoran Cothurnocystis bifida (Middle Cambrian, Utah, USA). The putative gill skeletons as viewed from the back side are indicated with an arrowhead. M is the putative mouth. The arrow indicates the posterior appendage. (B) The solute Coleicarpus sprinklei (Middle Cambrian, Utah, USA). The arrow indicates the posterior appendage, and the double arrow points to the single ambulacrum. (C) The helicoplacoid Helicoplacus (Early Cambrian, California, USA). The double arrow points to one of the ambulacral grooves. (D) The eocrinoid Gogia spiralis (Middle Cambrian, Utah, USA). The double arrow points to one of the five arms. (E) The edrioasteroid Edriophus bigsbyi (Ordovician, Ontario, Canada). It displays conspicuous pentameral symmetry; one of the arms is indicated by the double arrow. (F) The crinoid Dorycrinus mississippiensis (Mississippian, Indiana, USA). (G) The asteroid Furcaster palaeozoicus (Devonian, Budenbach, Germany). (H) The echinoid Bothriocidaris (Ordovician, Estonia). Scale bar, 0.5 cm in (A); 0.75 cm in (B) to (E); 2 cm in (F); 1.3 cm in (G); and 0.15 cm in (H). Part of a penny is shown for scale in (C).

That’s why I think these organisms are interesting ones, well worth the expense of a genome project, and much more. What have we learned so far? One important lesson I emphasize strongly is that having a genome sequence is only the very beginning: it is a collection of hard-earned raw data that is a tool for analysis and experiment and isn’t entirely an end in itself. With that in mind there are a few general results that I found fascinating, not entirely unexpected, and that complement our understanding of metazoan evolution.

  • The raw size of the genome is about 814 million bases (about a quarter the size of ours) and contains about 23,000 genes (about the same as ours, but because the count is the product of some automated procedures, expect that number to go down somewhat—still, it’s of the same order of complexity as ours). Keep in mind, too, that Strongylocentrotus purpuratus is a model organism, selected for properties that make it compatible with laboratory work, and probably has a stripped-down genome compared to other echinoderms. There’s nothing magically, amazingly sophisticated about the human genome—we are comparable in complexity to a purple algae-eater.

  • If you want to see into the machinery and puzzle out where the truly significant changes have been going on, what aspects of life had been most strongly affected by natural selection, you have to look into something we take for granted: the immune system. Echinoderms lack the adaptive immune system we have—that is, a set of genes that are rapidly modified somatically to generate a specific immune response—but have a greatly expanded, effective innate immune system. There is a separate paper on just the immune system of sea urchins; I think there are plans afoot to summarize that paper on the Panda’s Thumb.

  • Another significant difference is in the assembly of the skeleton. Vertebrates use calcium hydroxyapatite, while echinoderms use calcium carbonate (calcite), and there are suites of genes present in echinoderms and not us, and vice versa, all associated with these structures.

  • Sea urchins look to be deaf and blind with no discrete eyes or hearing organs, but they do have an unexpectedly rich repertoire of genes associated with sensory functions. These include a set of photoreceptor genes. They don’t have eyes, so they don’t have an image forming apparatus, but they do express opsins in their tube feet, which means they can at least have a general sensation of light levels and perhaps even wavelengths in their environment. The authors also report the presence of transcription factors involved in retinal development in vertebrates—what they’re doing in the retina-less echinoderm is unknown.

  • As you might guess, I’m most interested in the genes involved in development. Analysis of the RNA present in the mid- to late-gastrula stage showed transcripts of 12-13,000 genes…which would suggest that over half the genome is involved in the early events of development. It’s a provocative figure, but I have my doubts, given both the uncertainty of the actual total number of genes and the fact that assaying expression doesn’t necessarily mean that these genes are actually doing anything significant. I’ll believe a more robust developmental genetic analysis when it’s done.

  • Almost all of the known bilaterian transcription factors are represented in the urchin—no surprise there, and it just reinforces the idea of a general metazoan genetic toolkit. They report that 80% of the transcription factors are expressed in the gastrula, but again, I’ll refer you to the caveats in the previous point. That’s not at all impossible, though; we know that genes are pleiotropic and are reused over and over again at different stages of development.

  • One class of developmentally significant genes, the Wnt signalling factors, were singled out for study. The urchin has 11 of the 13 known Wnt subfamilies (vertebrates have 12 of 13), but with fewer representatives in each family. That means there is less redundancy in the signaling pathways, but the pathways are effectively all present, and the patterns of interactions are again probably roughly equivalent in complexity between the two phyla.

    (click for larger image)

    Survey of the Wnt family of secreted signaling molecules in selected metazoans. Each square indicates a single Wnt gene identified either through genome analyses or independent studies, and squares with a question mark indicate uncertainty of the orthology. Letter X’s represent absence of members of that subfamily in the corresponding annotated genome; empty spaces have been left for species for which genomic databases are not yet available.

I was unkind to those websites that played up the human disease connection in this research, but to be fair, the authors also emphasize it, in what I thought was a very unconvincing way.

The refinement of the inventory of vertebrate-specific or protostome-specific genes likewise benefits from the sea urchin genome. Many more human genes have shared ancestry across the deuterostomes, and in fact, bilaterian genes are more broadly shared than had been inferred from comparison of the previously limited genome sequences. The new biological niche sampled by the sea urchin genome provides not only a clearer view of the deuterostome and bilaterian ancestor, but has also provided a number of surprises. The finding of sea urchin homologs for sensory proteins related to vision and hearing in humans may lead to interesting new concepts of perception, and the extraordinary organization of the sea urchin immune system is different from any animal yet studied. From a practical standpoint, the sea urchin may be a treasure trove. Because of the many pathways shared by sea urchin and human, the sea urchin genome includes a large number of human disease gene orthologs. Many of the genes described in the preceding sections fall into this category and cover a surprising diversity of systems such as nervous, endocrine, and blood systems, as well as muscle and skeleton, as exemplified by the Huntington and muscular dystrophy genes. Continued exploration of the sea urchin immune system is expected to uncover additional variations for protection against pathogens. The immense diversity of pathogen-binding motifs encoded in the sea urchin genome provides an invaluable resource for antimicrobial applications and the identification of new deuterostome immune functions with direct relevance to human health. These exciting possibilities show that much biodiversity is yet to be uncovered by sampling additional evolutionary branches of the tree of life.

OK. Orthologs to genes involved in human disease leaves me cold; in most cases, we don’t understand how damage to these genes is generating the disease in humans, so I’m unclear on how identifying an ortholog to a human muscular dystrophy gene is going to add much to medicine just yet, even though it can be very useful in basic biology. The argument that the urchin immune system is obviously effective, yet with very different molecular components, and that can lead to new antimicrobial agents…that I find more promising.

But I still have to say that I’m disappointed that the paper ends on such an anthropocentric note. Echinoderms are extremely nifty in their own right, and we shouldn’t have to justify the work by going on and on about their utility to one species of ape.

Bottjer DJ, Davidson EH, Peterson KJ, Cameron RA (2006) Paleogenomics of Echinoderms. Science 314(5801):956-960.

Samanta MP, Tongprasit W, Istrail S, Cameron RA, Tu Q, Davidson EH, Stolc V. Sodergren E, Weinstock GM, Davidson EH, Cameron RA, Gibbs RA, Angerer RC, Angerer LM, Arnone MI, Burgess DR, Burke RD, Coffman JA, Dean M, Elphick MR, Ettensohn CA, Foltz KR, Hamdoun A, Hynes RO, Klein WH, Marzluff W, McClay DR, Morris RL, Mushegian A, Rast JP, Smith LC, Thorndyke MC, Vacquier VD, Wessel GM, Wray G, Zhang L, Elsik CG, Ermolaeva O, Hlavina W, Hofmann G, Kitts P, Landrum MJ, Mackey AJ, Maglott D, Panopoulou G, Poustka AJ, Pruitt K, Sapojnikov V, Song X, Souvorov A, Solovyev V, Wei Z, Whittaker CA, Worley K, Durbin KJ, Shen Y, Fedrigo O, Garfield D, Haygood R, Primus A, Satija R, Severson T, Gonzalez-Garay ML, Jackson AR, Milosavljevic A, Tong M, Killian CE, Livingston BT, Wilt FH, Adams N, Belle R, Carbonneau S, Cheung R, Cormier P, Cosson B, Croce J, Fernandez-Guerra A, Geneviere AM, Goel M, Kelkar H, Morales J, Mulner-Lorillon O, Robertson AJ, Goldstone JV, Cole B, Epel D, Gold B, Hahn ME, Howard-Ashby M, Scally M, Stegeman JJ, Allgood EL, Cool J, Judkins KM, McCafferty SS, Musante AM, Obar RA, Rawson AP, Rossetti BJ, Gibbons IR, Hoffman MP, Leone A, Istrail S, Materna SC, Samanta MP, Stolc V, Tongprasit W, Tu Q, Bergeron KF, Brandhorst BP, Whittle J, Berney K, Bottjer DJ, Calestani C, Peterson K, Chow E, Yuan QA, Elhaik E, Graur D, Reese JT, Bosdet I, Heesun S, Marra MA, Schein J, Anderson MK, Brockton V, Buckley KM, Cohen AH, Fugmann SD, Hibino T, Loza-Coll M, Majeske AJ, Messier C, Nair SV, Pancer Z, Terwilliger DP, Agca C, Arboleda E, Chen N, Churcher AM, Hallbook F, Humphrey GW, Idris MM, Kiyama T, Liang S, Mellott D, Mu X, Murray G, Olinski RP, Raible F, Rowe M, Taylor JS, Tessmar-Raible K, Wang D, Wilson KH, Yaguchi S, Gaasterland T, Galindo BE, Gunaratne HJ, Juliano C, Kinukawa M, Moy GW, Neill AT, Nomura M, Raisch M, Reade A, Roux MM, Song JL, Su YH, Townley IK, Voronina E, Wong JL, Amore G, Branno M, Brown ER, Cavalieri V, Duboc V, Duloquin L, Flytzanis C, Gache C, Lapraz F, Lepage T, Locascio A, Martinez P, Matassi G, Matranga V, Range R, Rizzo F, Rottinger E, Beane W, Bradham C, Byrum C, Glenn T, Hussain S, Manning FG, Miranda E, Thomason R, Walton K, Wikramanayke A, Wu SY, Xu R, Brown CT, Chen L, Gray RF, Lee PY, Nam J, Oliveri P, Smith J, Muzny D, Bell S, Chacko J, Cree A, Curry S, Davis C, Dinh H, Dugan-Rocha S, Fowler J, Gill R, Hamilton C, Hernandez J, Hines S, Hume J, Jackson L, Jolivet A, Kovar C, Lee S, Lewis L, Miner G, Morgan M, Nazareth LV, Okwuonu G, Parker D, Pu LL, Thorn R, Wright R. (2006) The Genome of the Sea Urchin Strongylocentrotus purpuratus. Science 314(5801):941-952.


  1. #1 KarenMcL
    November 13, 2006

    Does it say anywhere WHY they taste so Yummie in Sushi?

    Ummmm…Uni’s are one of my Favs!


  2. #2 Steviepinhead
    November 13, 2006

    Superficial as they were, I found the news reports enticing.

    But PZ’s much more in-depth review satisfied my aroused appetite! Thanks.

  3. #3 quork
    November 13, 2006


  4. #4 King Aardvark
    November 13, 2006

    Pointy, rather than fluffy, tribbles. Don’t make as good pets.

  5. #5 drwhore
    November 13, 2006

    Having used sea urchin embryos throughout my dissertation research, I am thrilled at this news. I know quite a few of the authors; one of them being a former labmate. I just wish it would have been done a couple years ago during my thesis research.

    Sadly, I also discovered that sea urchins don’t have all the usual transcription factors. Apparently, sea urchins don’t have a classical estrogen receptor. I studied the effects of estrogenic compounds on sea urchin development and could not locate an ER in the online genome (this was 2 yrs ago) nor could I isolate the gene with highly degenerate primers. However, estrogen does have an effect on development though even before embryonic transcription is turned on at hatching.

  6. #6 Tony
    November 13, 2006

    Anthropocentrism is a stance most authors have to take for funding purposes. It’s sad, but inevitable.

  7. #7 Scott
    November 13, 2006

    “… we shouldn’t have to justify the work by going on and on about their utility to one species of ape.”

    We shouldn’t, but many (or most) funding sources like to see some kind of “return” for their funding, which usually involves an effect on or for one species of ape. I’m sure there are lots of other creatures that are also interesting in their own right, but, as PZ notes as his first reason to care about urchins, this one is useful as “… one of the key model systems in developmental biology.” Even in this it is of utility to this species of ape. 😉

  8. #8 Jon D. Moutlon
    November 13, 2006

    I had hoped to view the linked “poster of highlinghts of sea urchin research”, but unfortunately it is available only to UMN Morris users.

  9. #9 Jon D. Moutlon
    November 13, 2006

    Oops, sorry, make that UMM.

  10. #10 SEF
    November 13, 2006

    They are lovely all the way to their middles! 😀

  11. #11 DrFrank
    November 13, 2006

    At a cursory glance, that picture of sea urchins looks a bit like a reasonably good fireworks display, which links in well to the whole celebratory aspect 🙂

  12. #12 AJ Milne
    November 13, 2006

    Excellent news.

    Can’t really relate to the anthropocentrism of the news reports. One of the things I like most about echinoderms is how very unlike us they are. From radial symmetry, through the way-cool hydraulics that make ’em move, through their on-another-temporal-level-entirely slow-mo lifestyle, they’re the aliens among us. Put that with their common ancestry, it’s just so neat to contemplate.

    One of the coolest pieces of video I’ve ever seen was a whole lot of sped-up footage of starfish hunting their prey on the ocean floor. They must have shot it over hours or days, then sped it way up, so you could see them hunting down hapless molluscs. Life and death and… well… slow speed chases. Can’t beat that for drama.

    Echinoderms. I like ’em.

  13. #13 dr. dave
    November 13, 2006

    Aaah… puts me in the mind of the old “Foreigner” song…

    “Urchin…. emergin’ sea urchin… emergin’ sea URCHIN (urchin-urchin-urchin…)”

  14. #14 Aesmael
    November 13, 2006

    AJ Milne: Link please? I’d like to see that!

  15. #15 AJ Milne
    November 13, 2006

    Re sped-up starfish: annoyingly, the video I saw was on PBS or somesuch, well prior to the Youtube era, and it doesn’t look like it’s made it to the web yet.

    But here’s a (very brief) bit of what it looked like. And I suspect this is a description of the actual video I saw. Might have been PBS’ The Shape of Life, as described in the article, since that clip does sound familiar. Quoting:

    Through high-definition video, time-lapse filming sped up 5,000 times, and motion control devices, the footage reveals creatures that appear motionless to the naked eye performing complex behaviors–sea anemones fight, starfish shove each other off rocks, and worms strangle each other… On the legs of a pier under Cannery Row, from the vantage point of a miniature camera hidden inside a mussel shell, viewers watch a sea star on the prowl. In sped-up time-lapse videography, the starfish takes on a whole new characteristic as it crawls up the pier post to a clump of mussels, and pries open a crack in one of the shells with hydraulic pressure from its thousands of tiny tube “feet.” A translucent white stomach floats out of the starfish underside and pushes into the mussel shell, where it digests its prey, still alive, into a soupy dinner.

    See also this bit… a sea star in motion in a tank. And this from Youtube.

  16. #16 AJ Milne
    November 13, 2006

    Hey, I can take it back! Some if it’s online, anyway. PBS put up the actual video described above–a starfish attacking a mussel. Browse to The Shape of Life: Digesting Mussels in the Shell and click on the video link.

    The other bit I remember was a starfish hunting down a snail. More of a chase thing, like I said.

  17. #17 djlactin
    November 14, 2006

    am i the only one amused (bemused? c-?) by the use of crosses to denote extinction?

  18. #18 Porlock Junior
    November 14, 2006

    Sea stars advancing on their prey. Oooo, creepy!
    I mean that, of course, in the most positive way. Thanks for the links.

  19. #19 The Ghost of Irony
    November 14, 2006


    Just because a species went extinct millions of years before god created the universe doesn’t mean it doesn’t deserve a good christian burial!

  20. #20 Monado
    November 14, 2006

    The symbol for “extinct” is supposed to be a dagger, not a cross. I think someone just looked at small blurry ones and translated them into graphic crosses rather than the special character “dagger.”

    BTW, the emphasis in the popular-press articles on how this research relates to humans and might benefit humans may be annoying, but it’s an axiom of communication that everyone is constantly tuned in to Radio WIIFM, “What’s in it for me?” and to catch their attention you have to broadcast on that wavelength. On a minority of readers are tuned in to the gee-whiz show of simple fascination with how the universe works. The rest want more tangible results.

  21. #21 DStopak
    November 14, 2006

    They never get cancer!

    And I bet they don’t get heart disease either.

  22. #22 Melissa
    November 14, 2006

    “It was a good soaking in echinodermiana.”

    PZ, I initially read this as “echinodermania.”

    I think I want a t-shirt now that says, “ECHINODERMANIA!”

  23. #23 TheBrummell
    November 14, 2006

    RE: anthropocentrism, two comments

    1. I’m currently TA-ing a 3rd-year Genetics course, and I’m stuck right into the middle of a huge pile of marking – formal lab reports about eye colour in Drosophila melanogaster. About two-thirds of these papers end with a statement about how useful studying fly eye colour genes will be to human disease applications. I doubt the students are getting this attitude from the primary literature (and requisite please-give-us-more-funding end comments), so I think it’s probably inherent. Monado’s reference to Radio WIIFM makes lots of sense in this context.

    2. Years ago, working a not-at-all-science summer job, I described to a co-worker some exciting Salmonid-olfactory research a PhD student I knew was conducting. She was angered by the mere idea that somebody would be researching something (using taxpayer money, of course) not directly relevant to commercial activity. She calmed down when I made up something about the importance of the salmonid fishery around here. The degree to which some people insist on a direct-benefit-right-now varies considerably, but my impression is mainly that the concept of the joy of knowledge is foreign to many.

  24. #24 Keith Douglas
    November 14, 2006

    Wow, what a lot of authors. I wonder what the record is?

    What’s next on the sequencing agenda? One of those species of bathroom molds that plague us?

  25. #25 Aesmael
    November 17, 2006

    Thank you, I am looking forward to checking those out.

  26. #26 Miguelito
    November 22, 2006

    This number of authours of this paper is far too excessive. I really wonder how many of those individuals contributed any text whatsoever and how many were lab rats simply involved in the collection of data.

  27. #27 Robert P.
    February 25, 2007

    I too wish this had been done a few years earlier, but I was able to access some of the early EST sequencing data at the tail end of my postdoc.

    The urchin and its gene regulatory network are a real boon to studying the interaction of different signaling pathways and I miss working on the little buggers.

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