NOAA Coral Reef Information System (CoRIS) - Professional Exchanges This Site NOAA Home Data & Publications Regional Portal About Coral Reefs Professional Exchanges Activities Glossary Home / Professional Exchanges Professional Exchanges Coral reef experts and enthusiasts from around the world use NOAA's Coral Health and Monitoring Program (CHAMP) listserve as a forum to discuss and debate a myriad of coral topics and issues. Discussions are lively and can last for weeks. This section presents some of these dynamic discussions among professionals. To join the coral-list see Coral-List -- NOAA's Coral Health and Monitoring Program listserver for coral reef research and news for information about the coral-list and instructions for subscribing. Sequencing a Coral Genome Corals vs. Rain Forests Should Acropora spp. Be Included on the Endangered Species List Deep water Corals A Future for Coral Reefs? The IndoPacific lionfish invasion of the U.S. south Atlantic sea coast and Caribbean Sea The Chagos Islands About CoRIS Data | Retired Pages | User Survey | Report Web Page Error | Privacy Policy Revised January 30, 2014 by Webmaster Site hosted by NOAA Coral Reef Conservation Program National Oceanic and Atmospheric Administration U.S. Department of Commerce http://coris.noaa.gov/exchanges/welcome.html http://www.coris.noaa.gov/exchanges/[11/25/2014 8:03:43 AM] NOAA Coral Reef Information System (CoRIS) - Professional Exchanges - Sequencing a Coral Genome This Site NOAA Home Data & Publications Regional Portal About Coral Reefs Professional Exchanges Activities Glossary Home / Professional Exchanges / Sequencing a Coral Genome The content on this web page was last updated in June of 2009. Some Read About: of the content may be out of date. For more information: http://coralreef.noaa.gov/. The Importance of Sequencing a Coral Update: Species A white paper for the National Institutes of Health's (NIH) Which Coral Species to National Human Genome Research Institute (NHGRI was Sequence? submitted in 2003 for the sequencing of the genome of Porites A Coral 'Laboratory lobata. This and follow-up documents, which included letters Rat' of support from about 50 investigators from around the world, reflected the prevailing wisdom that P. lobata was the Bibliography 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 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.” DNA molecule: A (Adenine), T (Thymine), C (Cytosine), G Click here for a list of discussion participants. (Guanine), S (Deoxyribose), P (Phosphate). (Credit: NHGRI) Click here for the summary of professional exchanges on coral Click image for larger view. genomics. http://www.coris.noaa.gov/exchanges/coralgenome/[12/1/2014 2:14:48 PM] NOAA Coral Reef Information System (CoRIS) - Professional Exchanges - Sequencing a Coral Genome 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 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 The lace coral, Pocillopora Cnidaria, a sister group to all the currently sequenced metazoans. The damicornis, is an inhabitant of sequenced genome would lay the foundation for all further molecular Indo-pacific coral reef communities. The species grow studies of coral biology. Of major interest to conservation biology as small, bushy-shaped would be the molecular mechanisms of stress and resistance, and also colonies. (Credit: Andrew the molecular machinery of mutualism between host corals and Bruckner, NOAA Fisheries) 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? 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 The Indo-pacific lobe coral, biochemical interfering substances that make it very difficult to apply Porites lobata, has branches molecular and biochemical techniques to many coral families. Finally, that form large lobes. The colonies may be huge, covering P. lobata and the mustard hill coral (P. asteroides) show a high degree several meters. (Credit: Bryan of similarity in many of their enzymes and genes, and it should be Harry, National Park Service, easy to adapt technologies that would utilize the gene sequence American Samoa) 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. (top) 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 http://www.coris.noaa.gov/exchanges/coralgenome/[12/1/2014 2:14:48 PM] NOAA Coral Reef Information System (CoRIS) - Professional Exchanges - Sequencing a Coral Genome consensus was reached about which single species or group should be sequenced first, but the participants were urged by some of their The great star coral, peers to lay aside their personal preferences and support the Montastraea cavernosa, grows as a mound-shaped colony in proposed project. Time was of the essence and the sequencing of the the tropical Atlantic waters. DNA of any coral would benefit all coral science and conservation (Credit: Andrew Bruckner, management. NOAA Fisheries) A Coral 'Laboratory Rat' 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,