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A white paper for the National Institutes of Health's (NIH) National Human Genome Research Institute (NHGRI
was submitted in 2003 for the sequencing of the genome of Porites lobata. This and follow-up documents,
which included letters of support from about 50 investigators from around the world, reflected the prevailing wisdom
that P. lobata was the preferred species for sequencing. A sequencing plan for P. lobata was submitted to NHGRI
for consideration in early 2005. Unfortunately, sequencing a coral genome was not seen as being a high priority
for NHGRI. The NIH Coordinating Committee believed that coral sequencing would be valuable for basic biology
and that P.lobata was probably the right choice of species. However, the Committee did not think, at that time, that sequencing
a coral genome was of direct enough significance for the general NIH mission.
Subsequently, genome sequencing studies of the Pacific coral, Acropora Millepora, have been conducted by Australian
and U.S.scientists. NHGRI provided the funding for the Acropora millepora genome survey sequence.
Sequencing a Coral Genome
DNA molecule: A (Adenine), T (Thymine), C (Cytosine), G (Guanine), S (Deoxyribose), P (Phosphate). (Credit: NHGRI) Click image for larger view.
The National Human Genome Research Institute (NHGRI) of the National Institutes of Health (NIH) is considering a $9 million proposal to sequence a coral genome. The objective of this effort is to identify all the genes in coral DNA, determine their sequences, store information in accessible databases, and compare them with reference DNA sequences in organisms which are better studied to understand gene function. Recent advances in gene sequencing, coupled with the relatively small size of many coral genomes (1.12 x 109 bp/haploid genome) will allow this to be accomplished relatively quickly with appropriate funding. This exchange on coral genome sequencing had three general topics: (1) the importance of sequencing the genome of a reef-building coral species, (2) the specific coral species to sequence, and (3) the concept of selecting a representative species as a coral lab rat.
Click here for a list of discussion participants.
Click here for the summary of professional exchanges on coral genomics.
Click here to download the complete unedited discussion (pdf, 245Kb).
Click here for a primer on molecular biology to help those unfamiliar with the subject matter of this exchange.
The Importance of Sequencing the genome of a Coral Species
The lace coral, Pocillopora damicornis, is an inhabitant of Indo-pacific coral reef communities. The species grow as small, bushy-shaped colonies. (Credit: Andrew Bruckner, NOAA Fisheries)
There was unanimous agreement on the importance of sequencing the genome of a reef-building coral species. Participants cited many benefits. The sequenced genome would provide a foundation for new avenues of coral scientific research and also provide a basis for technology development that could benefit coral resource management. It would yield major breakthroughs in phylogenetic systematics.
The sequenced coral genome would also be a major bonus for evolutionary genomics, since corals are representatives of the phylum Cnidaria, a sister group to all the currently sequenced metazoans. The sequenced genome would lay the foundation for all further molecular studies of coral biology. Of major interest to conservation biology would be the molecular mechanisms of stress and resistance, and also the molecular machinery of mutualism between host corals and zooxanthellae. The sequenced genome would make molecular techniques (e.g., microarrays) available to monitor the expressions of thousands of genes. For instance, genes expressed in normal versus stressed or diseased individuals could be identified, including genes that increase susceptibility or confer resistance to bleaching and disease.
Which Coral Species to Sequence?
The Indo-pacific lobe coral, Porites lobata, has branches that form large lobes. The colonies may be huge, covering several meters. (Credit: Bryan Harry, National Park Service, American Samoa)
There was no consensus on the best species for this first genome sequencing. However, several species were repeatedly advanced throughout the exchange. The authors of the proposal had selected the lobe coral, Porites lobata, in part because of its rising importance as a laboratory rat in coral exotoxicology, coral cell biology, coral immunity and coral neurophysiology. P. lobata was also chosen because of its widespread distribution in the Indian and Pacific Oceans, the Red Sea, and the Persian Gulf.
Another important advantage of Porites over others, such as the acroporids (elkhorn, staghorn and table corals) and star corals (Montastraea spp.), is that Porites lacks some of the various biochemical interfering substances that make it very difficult to apply molecular and biochemical techniques to many coral families. Finally, P. lobata and the mustard hill coral (P. asteroides) show a high degree of similarity in many of their enzymes and genes, and it should be easy to adapt technologies that would utilize the gene sequence information of P. lobata (e.g., polymerase chain reaction (PCR) gene array, enzyme-linked immunosorbent assay (ELISA), real-time PCR, and immunohistology) for further study of P. asteroides or other species of Porites.
The great star coral, Montastraea cavernosa, grows as a mound-shaped colony in the tropical Atlantic waters. (Credit: Andrew Bruckner, NOAA Fisheries)
In addition to Porites, species of Acropora (elkhorn corals), Montastraea (boulder star corals), and Pocillopora (lace corals) were the principal ones advanced as candidates for sequencing. Each of these species was favored for a variety of reasons, including geographic distribution, ecological and economic importance, amenability to molecular techniques, ease of laboratory rearing, growth rate, survivability, susceptibility to disease, and others. No consensus was reached about which single species or group should be sequenced first, but the participants were urged by some of their peers to lay aside their personal preferences and support the proposed project. Time was of the essence and the sequencing of the DNA of any coral would benefit all coral science and conservation management.
A Coral 'Laboratory Rat'
Another view of a great star coral, Montastraea cavernosa, colony. (Credit: NOAA)
There was considerable discussion exploring the concept of a coral lab rat, a genetically known strain that could be laboratory-reared, mass cultured, and shipped easily with a high chance of survival to any laboratory in the world. Model corals would enable rapid advances by focusing research on fundamental biological concepts broadly applicable across the taxon. Scientists could take advantage of the favorable attributes of this strain to study processes in molecular, cellular, developmental, physiological, and environmental biology. Most of the discussion on this topic focused on the specific characteristics that would be desirable in such a species. There was unanimous agreement among the participants that the coral lab rat concept was important and should be pursued. Model corals must be representative of coral diversity, and include Indopacific and Caribbean species, autotrophs and heterotrophs, branching, massive and plating species, and species with different algal symbionts. Because of the corals' evolutionary history, which suggests that extant corals are not a monophyletic group and different families can be both ecologically and physiologically very different, no single species would be representative of corals in general.
Bruckner, Andrew. Spring 2002. Life-Saving Products from Coral Reefs. Issues in Science and Technology Online.
The Human Genome Project, 1990-2003. 2003. Genomics and Its Impact on Science and Society: The Human Genome Project and Beyond. U.S. Department of Energy Human Genome Program.