Genotoype-by-sequencing of three geographically-distinct populations of the Olympia oyster, Ostrea lurida
A genotype-by-sequencing approach to sequence 32 individuals from each of three geographically-separated Olympia oyster populations (Dabob Bay, Fidalgo Bay, Oyster Bay). Gentopying and SNP identification from these three populations may be used in restoration efforts to evaluate the possibility, and the effects, of gene flow within Olympia oyster populations around the Puget Sound (Washington, USA).    Oysters (n=32) were obtained from three bays within Puget Sound, WA: Fidalgo Bay (48°28'31.1"N 122°34'48.6"W), Dabob Bay (47°49'27.4"N 122°48'37.9"W), and Oyster Bay (47°06'21.2"N 123°04'32.8"W). Oysters were shucked into 1.5mL tubes and stored -80C.    Sample preparation, library construction, and sequencing were performed by the Beijing Genomics Institute (BGI; Beijing, China). Isolation of DNA was performed via the salting out method. Briefly, tissue was lysed with Proteinase K, followed by ethanol precipitation of nucleic acids. Sample DNA was examined for integrity via agarose gel.    Oyster DNA and Illumina adapters containing barcodes were digested with ApeKI restriction enzyme (recognition site: GCWGC). Adapters were ligated to digested oyster DNA, with each individual oyster receiving a unique barcode. These libraries were pooled and subjected to polymerase chain reaction (PCR). Average insert size (219bp) was determined via Bioanalyzer (Agilent Technologies). This pool was sequenced on a HiSeq 4000 (Illumina) as an 100bp paired-end run.    Identification of individuals, explanations of sample nomenclature, and a list of indices used for sequencing/demultiplexing can be found in this dedicated GitHub repository: https://github.com/RobertsLab/project-olympia.oyster-genomic/wiki/Genotype-by-sequencing-November-2015
University of Washington
Oly_BGI_GBS