oyster genome sequence

Image of fresh Pacific oyster courtesy of Guofan Zhang, photo by Tao Liu

The world of the mollusk genome is now our oyster, as researchers have now sequenced the genetic code of this hearty (and delicious) shellfish, revealing it to be even more complex and adaptable than previously imagined.

The new genome provides insights how oysters manage to cope with a dynamic habitat and how they build their shells. The genome of the Pacific oyster (Crassostrea gigas) contains approximately 28,000 genes (compared with the 20,000 or so genes of humans), some 8,654 of which are thought to be specific to oysters—or at least to mollusks.

One of the big mysteries surrounding oysters and many other mollusks is how they manage to thrive in such variable marine environments. As sessile creatures that largely stay put, they endure extreme temperature changes, swings in salinity, and prolonged exposure to open air in the intertidal zone. The researchers found 88 different genes that code for so-called heat shock protein 70, which guards cells and tissue against hot temperatures. This extra buffering might explain why oysters can survive in the sun in temperatures up to about 49 degrees Celsius (120 degrees Fahrenheit). By contrast, humans have about 17 genes that make this protein, and even relatively immobile sea urchins have just 39.

Oysters are known for being excellent water filterers, and some environmental groups have even proposed reintroducing these shellfish to New York City waterways to clean up the harbor. How can these oysters stay healthy with so many chemicals and heavy metals flowing through them? The genome reveals one of the oyster's secrets: a highly active immune system—especially in its gut. The researchers found that many of the genes that make immune-related proteins are expressed in the oyster's so-called digestive gland, "indicating that the digestive system of this filter feeder is an important first-line defense organ against pathogens," the authors noted in their paper published online September 19 in Nature (Scientific American is part of Nature Publishing Group).

Perhaps the key to the survival of this soft-bodied organism is its flexible genome. The researchers sequenced 61 transcriptomes (RNA in the cell or tissue) and then exposed them to familiar oyster stressors. When exposed to air, for example, 4,420 different genes altered their expression. And some exposures produced impressive results. Exposing the transcriptomes to heat invoked a roughly 2,000 times higher expression of five of the heat shock protein 70-coding genes.

The genome of the oyster, the first mollusk to be sequenced, also cracked open some evolutionary clues about the shell of these tenacious bivalves. Once thought to be a fairly simple, self-assembling matrix of calcium carbonate, it now looks to be a complex creation that has undergone eons of evolutionary tweaking. And it shares some surprising signatures with the cell walls of other animals, suggesting that shell formation is an active and elaborate process that involves hundreds of proteins.

The oyster genome had thwarted standard sequencing techniques because it repeats itself in many places—and in others has different codes in the same places in a single individual. So the researchers tried a "fosmid-pooling" strategy, which allowed them to divide the genome up and compare multiple sequencings of each area. To help the process along further, they also created a more genetically homogenous oyster, using one from four generations of direct sibling inbreeding. They then compared this to a wild-caught oyster, just to make sure their results were not too altered by the chosen individual.

The success with the oyster genome will help open the door to sequencing more of the highly diverse mollusks, including snails, scallops and, perhaps even the master RNA editors themselves, the octopuses. Information from the oyster genome and other sequences in this group could help researchers better understand these organisms' role in the oceans, their evolution and how they respond to climate change and ocean acidification as well as better strategies for raising them.