JCVI Researchers Collaborate on Sequence and Analysis of First Pennate Diatom Genome
Hundreds of Bacterial Genes Found in Phaeodactylum tricornutum Genome
LA JOLLA, CA — October 15, 2008 — The genome of Phaeodactylum tricornutum has been sequenced and analyzed by a large international team of researchers led by U.S. Department of Energy Joint Genome Institute (DOE JGI) and the Ecole Normale Supérieure of Paris. The group also includes scientists from the J. Craig Venter Institute. The team was led by first author Chris Bowler, Ph.D., of the Ecole Normale Supérieure, and published results in the October 15 edition of Nature. This is only the second diatom and the first of the pennate class to be sequenced and published.
Diatoms are eukaryotes that have a unique cell wall made from silica. They are keys to better understanding the environmental health of the marine ecosystems since they are the major residents in the world's waters and are responsible for most of the regulation of carbon and production of oxygen in these waters.
Researchers compared the P. pseudonana genome to the previously sequenced diatom, Thalassiosira pseudonana to further understand diatom evolution, function and prevalence. P. tricornutum has 27.4 million base pairs of DNA, and 10,402 genes making it slightly smaller than T. pseudonana.
JCVI researchers, Andrew Allen, Ph.D., and Jonathan Badger, Ph.D., developed novel phylogenomic profiling techniques to identify the origins of the diatom genes. Surprisingly, they found that more than 300 of these genes were of bacterial origin. This finding has significant implications in understanding diatom evolution and should enable better understanding of how diatoms utilize nutrients found in their environments.
Bowler and his colleagues are also trying to understand the role that iron plays in the Phaeodactylum's development. Iron is even more precious than nitrogen in the ocean and its absence in the southern hemisphere is likely a major cause of oceanic deserts of photosynthesis there. Bowler's team has demonstrated that when iron deficiency occurs processes such as photosynthesis and nitrogen assimilation are suppressed.
Recently, Allen, Bowler and colleagues published a paper in the journal PNAS describing how diatoms metabolize iron and how they adapt to low iron environments. In this study, the team determined that some of the genes responsible for the diatoms' abilities to survive in low iron availability are bacterial and that diatoms appear to have a bacterial-like iron binding protein.
JCVI researchers are funded by NSF grants in the Biological Oceanography and Microbial Genome Sequencing programs.
About the J. Craig Venter Institute
The JCVI is a not-for-profit research institute in Rockville, MD and La Jolla, CA dedicated to the advancement of the science of genomics; the understanding of its implications for society; and communication of those results to the scientific community, the public, and policymakers. Founded by J. Craig Venter, Ph.D., the JCVI is home to approximately 400 scientists and staff with expertise in human and evolutionary biology, genetics, bioinformatics/informatics, information technology, high-throughput DNA sequencing, genomic and environmental policy research, and public education in science and science policy. The legacy organizations of the JCVI are: The Institute for Genomic Research (TIGR), The Center for the Advancement of Genomics (TCAG), the Institute for Biological Energy Alternatives (IBEA), the Joint Technology Center (JTC), and the J. Craig Venter Science Foundation. The JCVI is a 501 (c) (3) organization. For additional information, please visit http://www.JCVI.org.
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