The mitochondrial genome of the eastern oyster, Crassostrea virginica: The complete DNA sequence and its application in local restoration efforts

The eastern oyster, Crassostrea virginica, is an economically important species throughout its range from the Gulf of St. Lawrence, Canada to the Yucatan Peninsula, Mexico. Oyster harvesting in the Chesapeake Bay was once a lucrative fishery and a major component of the local economy for more than a century. Concurrent with overexploitation, the oyster population has been subject to high mortality from epizootics caused by the parasites MSX and Dermo. The result is a critically low abundance, diminishing the status of the species as an economic and ecological resource. The Chesapeake Bay oyster population is an estimated 1% of its size a century ago and sustainable harvesting is no longer feasible. Several management options for rehabilitating local oyster populations have been considered, though an effective solution remains to be determined. Enhancement of native populations through spawner transplantation is a well-established approach. Seeding an area with hatchery-reared, genetically superior, disease-resistant oysters will potentially enhance survival and propagation of the native oyster populations. The enhancement of resident populations by transplanting hatchery-reared oysters is arguably the best option for oyster restoration available at this time.; The recent use of high-throughput molecular genetic techniques in monitoring restoration effort has proven to be informative, accurate and cost-effective. Techniques for detecting single nucleotide polymorphism (SNP) are quickly becoming dominant tools in molecular biology, particularly in the areas of human disease and population biology. The application of SNP technology to assess polymorphism in mitochondrial DNA (mtDNA) has received less attention but is an area of great promise. Genetic drift is often quite pronounced in mtDNA. Because mitochondria have a high replication rate and lack DNA repair mechanisms, the rate of mutation is typically higher in mtDNA than in nuclear DNA. In a preliminary study, I estimated the mitochondrial mutation rate in oysters to be at 6.2 x 10-5 nucleotide substitutions per site per generation. The high mutation rate results in high genetic variability that can be useful in the detection of hatchery-specific mitochondrial markers. Particular patterns of mitochondrial markers (or haplotypes) provide us with unique genetic signatures that can be useful in evaluating the success of restoration efforts.; This research project comprises three parts. In the first part, I sequenced and annotated the complete mitochondrial genome of the eastern oyster, C. virginica. Complete sequence data provide essential background knowledge necessary in project design for subsequent investigations including determination of regions to be used for analysis, primer development, and finally identification of potential molecular markers for use in restoration assessment. The second component assessed natural rates of mutation in the mitochondrial genome. The last component identified polymorphic markers capable of distinguishing hatchery-produced spat outplanted in the Little Choptank River (Chesapeake Bay, Maryland) from resident oysters. These markers were used to assess the survival and recruitment contribution of the restoration effort in the Little Choptank River.