The case for sequencing the Pacific oyster genome

Type Article
Date 2005-08
Language English
Author(s) Hedgecock Dennis1, Gaffney Patrick M.2, Goulletquer PhilippeORCID3, Guo Ximing4, Reece Kimberly5, Warr Gregory6
Affiliation(s) 1 : Univ South Calif, Dept Biol Sci, Los Angeles, CA 90089 USA.
2 : Univ Delaware, Coll Marine Studies, Lewes, DE 19958 USA.
3 : Inst Francais Rech Exploitat Mer, F-17390 La Tremblade, France.
4 : Rutgers State Univ, Inst Marine & Coastal Sci, Haskin Shellfish Res Lab, Port Norris, NJ 08349 USA.
5 : Coll William & Mary, Sch Marine Sci, Virginia Inst Marine Sci, Gloucester Point, VA 23062 USA.
6 : Med Univ S Carolina, Hollings Marine Lab, Charleston, SC 29412 USA.
Source Journal of Shellfish Research (0730-8000) (National Shellfisheries Association), 2005-08 , Vol. 24 , N. 2 , P. 429-441
WOS© Times Cited 78
Keyword(s) Genomics, Evolutionary and ecological, Nucleotide diversity, Lophotrochozoa, Crassostrea gigas genome sequence, Pacific oyster
Abstract An international community of biologists presents the Pacific oyster Crassostrea gigas as a candidate for genome sequencing. This oyster has global distribution and for the past several years the highest annual production of any freshwater or marine organism (4.2 million metric tons, worth $3.5 billion US). Economic and cultural importance of oysters motivates a great deal of biologic research, which provides a compelling rationale for sequencing an oyster genome. Strong rationales for sequencing the oyster genome also come from contrasts to other genomes: membership in the Lophotrochozoa, an understudied branch of the Eukaryotes and high fecundity, with concomitantly high DNA sequence polymorphism and a population biology that is more like plants than any of the model animals whose genomes have been sequenced to date. Finally, oysters play an important, sentinel role in the estuarine and coastal marine habitats, where most humans live, environmental degradation is substantial, and oysters suffer intense fishing pressures and natural mortalities from disease and stress. Consumption of contaminated oysters can pose risks to human health from infectious diseases. The genome of the Pacific oyster, at IC = 0.89 pg or similar to 824 Mb, ranks in the bottom 12% of genome sizes for the Phylum Mollusca. The biologic and genomic resources available for the Pacific oyster are unparalleled by resources for any other bivalve mollusc or marine invertebrate. Inbred lines have been developed for experimental crosses and genetics research. Use of DNA from inbred lines is proposed as a strategy for reducing the high nucleotide polymorphism, which can interfere with shotgun sequencing approaches. We have moderately dense linkage maps and various genomic and expressed DNA libraries. The value of these existing resources for a broad range of evolutionary and environmental sciences will be greatly leveraged by having a draft genome sequence.
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Hedgecock Dennis, Gaffney Patrick M., Goulletquer Philippe, Guo Ximing, Reece Kimberly, Warr Gregory (2005). The case for sequencing the Pacific oyster genome. Journal of Shellfish Research, 24(2), 429-441. Open Access version :