Genome of the lowly oyster is likely to tell us a lot

September 19, 2012

What’s it like to be half-asphyxiated twice a day, suffer through 90-degree swings in temperature and be forced to eat everything that happens to come by your mouth?

Welcome to life as an oyster.

Starting today, biologists have a clearer window into what it takes for complex organisms to survive — and flourish — under such difficult circumstances.

An international team of 75 researchers on Wednesday published the full genome — the entire DNA message — of the Pacific oyster. The toothsome Crass­ostrea gigas is the first mollusk whose genome has been fully sequenced.

The information will shed light on the biology and evolution of one of the planet’s largest animal phyla, with more than 100,000 species. Mollusks comprise the largest category of animals in the world’s oceans.

More than 180 species have fully sequenced genomes. The best-known is the human genome, completed in 2003.

Most of the sequenced organisms are microscopic — bacteria, fungi, protozoans. But larger organisms of commercial, cultural or medical interest have also been done. The latter include the dog, the cat, the cow, the rat, the mouse, the mosquito and the honeybee, as well as lab workhorses such as the fruit fly and the transparent roundworm.

Comparing genomes helps scientists understand the levers and gears driving activities special to certain types of organisms as well as the essential tasks shared by most (or all) of them.

C. gigas is the most commonly eaten oyster in the world, collected or grown on the Pacific coast of North America, Europe, East Asia and Australia. Analysis of its genome, which has just begun, is likely to have both scientific and practical benefits.

For example, a close look at the genes of its immune system might help reveal why the Pacific oyster is largely resistant to MSX, a protozoan parasite that has decimated the Eastern oyster, C. virginica, in Chesapeake Bay.

“It’s not the same as having the Eastern oyster genome in front of us,” Patrick M. Gaffney, a marine biologist at the University of Delaware, said of the project, which he participated in. “But this gives us a framework for looking at specific regions of the Eastern oyster genome.”

If disease-resistant genes are identified, they could lead to a “molecular breeding” program in which oysters carrying them are raised in large numbers and used in aquaculture.

Shell is the oyster’s most obvious feature. How shell forms, however, is still something of a mystery. Understanding the process could lead to the production of artificial “bioceramics.”

But it’s the genome’s window on basic biology that could prove most valuable in the long run.

As a filter-feeder, the oyster has little choice but to ingest whatever’s in the water, including viruses, bacteria, sediment and metals. Its “digestive gland” is loaded with active immune-system genes, according to the first-pass analysis of the genome, published in the journal Nature.

Understanding what those genes do will shed further light on “innate immunity,” a primitive form of cellular defense that was the subject of last year’s Nobel Prize in Physiology or Medicine.

The oyster genome’s most important lessons may be about surviving changing conditions, which all organisms face but few as dramatically as oysters.

“They have an exceptional abil­ity to tolerate environmental stress,” said Ximing Guo, a professor of marine science at Rutgers University who led the project with Guofan Zhang of the Institute of Oceanology of the Chinese Academy of Sciences.

Oysters can tolerate 100-degree water but also can withstand being covered with ice. They can survive out of water for weeks, if kept cool. They inhabit water whose salinity varies seven-fold depending on season and weather.

All that’s possible because they are specialists in inhibiting “apoptosis,” the process by which a cell kills itself in an orderly fashion once it suffers serious damage. This is a hot topic in biology, as it sheds light on both disease and aging.

Pacific oysters have 48 genes coding for proteins that inhibit apoptosis. The human genome has eight.

“That is something that is very surprising,” Guo said. “We thought they had a primitive system regulating this, one not as advanced as vertebrates.”

The oyster genome might even shed light on the possible consequences of climate change, which scientists fear could threaten marine organisms’ ability to form shells as the ocean becomes more acidic.

Initial analysis of the genome, however, provides evidence that the shell crystals start growing inside cells, where acidity can be controlled by the organism, not outside them.

“Ocean acidification is still a threat, but the impact may be less than we think, at least when it comes to shell formation,” said Andrew S. Mount, a researcher at Clemson University and an author of the paper, published in the journal Nature.

The Pacific oyster genome has about 800 million pairs of DNA nucleotides, compared with 3 billion in the human genome. Oysters, however, have more genes than do people — 28,000 versus about 20,000.

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