By Ewen Callaway of Nature magazine

One of the coral species hit hardest by climate change has become the first to have its genome published. The genome of the branching coralAcropora digitifera appears online today in Nature. The draft sequence of a related species common on Australia's Great Barrier Reef, the staghorn coralAcropora millepora, was released online earlier this month, prior to formal publication.

Corals are under threat from environmental change caused by global warming -- which has led to warmer, more acidic oceans -- as well as from disease and other stresses. David Miller, a coral biologist at Queensland's James Cook University in Townsville, Australia, who is leading the A. millepora project and is a co-author on the A. digitifera paper, says the advent of information from coral genomics won't necessarily save these particular species. But their genomes are helping scientists to identify genes responsible for coping with environmental stress in corals, and might eventually feed into coral conservation efforts.

The two sequenced species, like other corals, are cniderian invertebrates that live in a cosy symbiotic relationship with algae called zooxanthellae, dinoflagellate organisms that give corals their colour. Under stressful environmental conditions, the algae die or lose their pigmentation, causing the coral to turn white and die, too -- a process known as bleaching. Both A. digitifera and A. milleporahave been particularly affected.

Special relationship

Among the 420 million nucleotides in the A. digitifera genome lies a possible explanation for its dependence on symbiotic algae. When lead author Nori Satoh and his team at the Okinawa Institute of Science and Technology in Onna, Japan, were describing the coral's nearly 24,000 genes, they noticed that the animal lacks a gene involved in making an essential amino acid called cysteine.

Analyses of DNA and RNA in two other species of Acropora reveal that they also seem to have shed this gene, which encodes the enzyme cystathionine beta-synthase. Satoh proposes that the coral must live with its dinoflagellate to get a supply of cysteine, an essential ingredient in many proteins. Miller notes that other coral species have the genetic machinery to make cysteine, but he speculates that other missing biochemical pathways could keep them wedded to their own dinoflagellates.

Other characteristics of the A. digitifera genome fit in with its symbiotic existence. The coral has a wealth of immune-related genes responsible for recognizing and responding to pathogens -- far more than its nearest sequenced ancestor, the sea anemoneNematostella vectensis. "Because these [corals] are colonial symbiotic animals, they really need a much more sophisticated way of differentiating friend from foe," Miller suggests.

Satoh's team discovered that corals and sea anemones last shared a common ancestor about 500 million years ago -- 260 million years before modern coral reefs appear in the fossil record. A closer look at the genome also solved a long-standing mystery: it is the corals themselves, not their dinoflagellate residents, that make other types of amino acids that protect the corals from ultraviolet light and act as a sun screen.

Genomic riches

Steven Vollmer, a coral biologist at Northeastern University's Marine Science Center in Nahant, Massachusetts, says the ability to answer such questions is precisely why a coral genome is needed. "We can no longer fall back on saying, 'Oh, I don't know that because we don't have a genome'," he says.

"There are infinite possibilities with what you can do once you have a coral reference genome," he adds. For instance, Vollmer has already collected gene-expression data from a related species of Caribbean staghorn coral, and the Acropora genome sequences will allow him to quickly identify the coral genes and sift out those from the dinoflagellate. (The draft A. millepora genome should permit similar analyses, though because that data is unpublished, it currently has a restriction that means researchers can't publish results of any gene expression mapping onto the A. milleporasequence).

As for Miller and his team, they are focusing on the innate immune response ofA. millepora, which he says resembles that of vertebrates. His team is also studying the evolution of coral genes involved in recognizing other corals, symbiotic dinoflagellates and parasites.

None of these studies is likely to save corals from continued bleaching. But Miller believes that identifying genes and gene variants that allow some populations to withstand warmer, acidic oceans could feed into conservation efforts.

Many species of corals can be reared in aquaria, and researchers are studying how corals transplanted from the southern stretches of the Great Barrier Reef fare in warmer waters to the north. "It opens the door to selective breeding and all kinds of things," says Miller of the genome sequences. "That's a long way off, but at least it becomes a real possibility."

This article is reproduced with permission from the magazine Nature. The article was first published on July 24, 2011.