Virtual squirtlet

Sea squirts are not the most endearing creatures, but they are pretty interesting in their own way. Although their adults are basically cellulose-covered bags of jelly, their larvae and their genomes reveal their dirty secret: they are actually close (probably the closest) relatives of vertebrates. Squirts and their kin – collectively known as tunicates – also have some of the fastest-evolving, most crazily scrambled genomes among animals (e.g. Denoeud et al. 2010).

(Say hi to your long-lost cousins! A whole crowd of grown-up Ciona from Wikipedia)

To be fair, not all of them are as bland and ugly as Ciona species. Some of them are actually quite gorgeous with all the colourful extravagance you’d expect from a tropical marine invertebrate (below is one example from Wikipedia’s squirt entry).

But, anyway, I got a bit carried away there. In truth, I just wanted to squee about a new virtual squirt embryo (Nakamura et al., 2012). Because 3D reconstructions of animals down to single-cell resolution are pretty damn cool.

Unlike the adults, baby squirts actually look a proper chordate, with a plump little body and a long tail supported by a good old notochord. They float in their little eggs for a while, developing their tails and simple sensory systems, and then they swim around for a few days before settling and transforming into those unappealing jellybags for a life of filter-feeding and spawning. (Below: the tadpole larva of the colonial squirt Botryllus schlosseri by Richard Grosberg via this site)

Because squirts are so close to vertebrates, and some of them (like Ciona) are relatively easy to breed and grow up in the lab, they’re among the favourite model organisms of evo-devo researchers. That means some people are bound to put serious effort into community resources about them. The good folks at Keio University in Japan have been building this amazing resource for years, where they painstakingly document the development of Ciona intestinalis from fertilised egg all the way to jellybaghood using photographs, microscopic images and 3D reconstructions from optical sections made with a confocal microscope. The virtual embryo is the latest addition to this project. It represents a stage where the embryo is growing its tail, and it is packaged into an interactive PDF with all sorts of annotations on cell types and stuff (that my PDF viewer can’t handle :(). I’m not much into sea squirts, but an interactive embryo you can manipulate and examine cell by cell and use as a free reference to interpret your own experimental results? That’s seriously awesome.

(Almost as cool as the digital zebrafish embryo movies)

(Above: A, an example of the confocal images used to build the virtual squirt, with a few views inside the 3D model: B, rear view of the “skinned” virtual embryo, C, side view of same, and D, virtual cross-section of the tail. Tissues like muscle, notochord and nerve tube are colour-coded and labelled. From Nakamura et al. [2012])



Denoeud F et al. (2010) Plasticity of animal genome architecture unmasked by rapid evolution of a pelagic tunicate. Science 330:1381-1385

Nakamura MJ et al. (2012) Three-dimensional anatomy of the Ciona intestinalis tailbud embryo at single-cell resolution. Developmental Biology in press, available online 27/09/2012, doi: 10.1016/j.ydbio.2012.09.007


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