A crustacean genome at last

Daphnia pulex; (Photo: Paul Hebert)

This week saw the official publication of the first crustacean genome (unless you count the flying crustacean genomes: fruit flies, bees, wasps, aphids, mosquitoes, and beetles). The genome is that of a “water flea” Daphnia pulex, a Branchiopod related to brine shrimp (Arthemia) and fairy shrimp (Triops). Daphnia is tiny, between 1.5 and 3 millimeters in length. They live in fresh water where they forage for algae and are preyed upon by fish. Daphnia are also an ecologically useful indicator species because they respond strongly to environmental contamination. Therefore, they have been studied extensively, and much is known about their ecology, behavior, and interaction with the environment; much more, in fact, than many other model organisms.

Their importance to ecological research, and the lack of a sequenced crustacean genome, made Daphnia an attractive target for genome sequencing and assembly. The reseachers found that Daphnia’s genome has 200 million bases (to our 3 billion), comprising 30,907 genes (to our 23,000). Therefore, compared to humans, Daphnia has more genes packed into a smaller genome. It seems that there has been rampant gene duplication in this animal creating tandem arrays of similar genes (called paralogs); recently duplicated, but gradually diverging evolutionarily. The genes in these arrays are typically located close together, and have little “junk DNA” within in them; resulting in a small, but gene-rich genome. Daphnia may selectively express (turn on) specific genes from these duplication clusters depending on the demands of their environment. Imagine this concept as drawers in a tool chest. One drawer may contain a whole spectrum of slightly different, but functionally similar drill bits. If you need to drill a quarter inch hole, you can grab just the right bit for the job. With this new wealth of genomic data, future research can peer deeper into the interplay between environmental factors and gene expression (You can read more about this facet of the Daphnia genome at Deep Sea News).

Daphnia’s genome is also interesting to those who study the genetics behind crustacean vision. There has been a good deal of behavioral and physiological vision work done on Daphnia. Adult Daphnia have a single cycloptic eye with a grand total of 22 ommatidia: the individual facets of a compound eye. This essentially equates to a photoreceptive array of 22 pixels with which to visualize their environment.

The compound eye of Daphnia magna, a similar species to D. pulex. Inset is a drawing of the eye structure, viewed slightly off-axis (dotted line). The white areas are lens facets and the dark area is the retina. Adapted from Smith and Macagno 1990.

Regardless of the diminutive resolution of their eye, behavioral studies have shown that Daphnia are capable of both color and polarization vision, and have at least four spectral classes of photoreceptors (ultraviolet, blue, green, and red). Pretty good for 22 pixels, right? Well, the genome of this animal holds another surprise about their visual system: it contains 46 opsins; the primary component of a visual pigment. Visual pigments are the molecules in photoreceptors that translate various colors (wavelengths) of light into cellular signals.

What the heck is a tiny crustacean, with a tiny eye, doing with all those opsins? We humans have a total of nine opsins in our genome; four are involved in vision, one is a time-keeper for circadian rhythms, and the rest are poorly understood proteins expressed in the deep brain and retina. As with many other genes in Daphnia’s genome it seems that opsins have also undergone tandem duplication events, resulting is large suites of closely related opsin genes. Unfortunately, we need to find out where in the eye, and when, each of these opsins is used in order to discover if their expanded numbers hold any functional significance.

Interestingly, rampant opsin duplication may not be unique to these water fleas. Mantis shrimp, which I work on, also appear to have many more opsins than they should need to produce their sixteen photoreceptor types. The gene tree below shows the relationships of just one class of opsins expressed in mantis shrimp eyes. Each color represents a different species of mantis shrimp. Notice that some species have up to twelve different opsins in this class, and many of these are related most closely to other opsins from the same species; this is indicative of recent duplications similar to those found in the Daphnia genome.

A gene tree of mantis shrimp opsins. Each color represents an opsin for a certain species of mantis shrimp. Adapted from Porter et all., 2009.

Perhaps huge suites of opsins are the rule, rather than the exception, in crustaceans. There could be tremendous hidden opsin diversity in these animals that was previously missed by researchers. It will be exciting to figure out the evolutionary and ecological significance of massive opsin duplications. Do crustaceans have special opsins for every season, depth, and time of day? Or are these genes unused, or functionally identical to one another, making their presence little more than random evolutionary noise; the products of nature throwing spaghetti at a wall to see what sticks?

I predict that it will be exciting to find out!


  • Colbourne, J., Pfrender, M., Gilbert, D., Thomas, W., Tucker, A., Oakley, T., Tokishita, S., Aerts, A., Arnold, G., Basu, M., Bauer, D., Caceres, C., Carmel, L., Casola, C., Choi, J., Detter, J., Dong, Q., Dusheyko, S., Eads, B., Frohlich, T., Geiler-Samerotte, K., Gerlach, D., Hatcher, P., Jogdeo, S., Krijgsveld, J., Kriventseva, E., Kultz, D., Laforsch, C., Lindquist, E., Lopez, J., Manak, J., Muller, J., Pangilinan, J., Patwardhan, R., Pitluck, S., Pritham, E., Rechtsteiner, A., Rho, M., Rogozin, I., Sakarya, O., Salamov, A., Schaack, S., Shapiro, H., Shiga, Y., Skalitzky, C., Smith, Z., Souvorov, A., Sung, W., Tang, Z., Tsuchiya, D., Tu, H., Vos, H., Wang, M., Wolf, Y., Yamagata, H., Yamada, T., Ye, Y., Shaw, J., Andrews, J., Crease, T., Tang, H., Lucas, S., Robertson, H., Bork, P., Koonin, E., Zdobnov, E., Grigoriev, I., Lynch, M., & Boore, J. (2011). The Ecoresponsive Genome of Daphnia pulex Science, 331 (6017), 555-561 DOI: 10.1126/science.1197761
  • Porter ML, Bok MJ, Robinson PR, & Cronin TW (2009). Molecular diversity of visual pigments in Stomatopoda (Crustacea). Visual Neuroscience, 26 (3), 255-65 PMID: 19534844
  • Smith KC, Macagno ER (1990) UV photoreceptors in the compound eye of Daphnia magna (Crustacea, Branchiopoda). A fourth spectral class in single ommatidia. J Comp Physiol A, 166, 597-606.


  1. Michael Bok says:

    Very nice cuttlefish. I’ve always enjoyed your word-craft!

  2. […] Mimic #10 Followup February 8, 2011 Michael BokMonday Mimic #10 February 7, 2011 Michael BokA crustacean genome at last February 6, 2011 Michael BokThe Birds, the Bees, and Feeding the WorldWhat will happen to the fish? […]