Graduate student Danielle Dodge recently travelled to Catalina Island, CA to attend a 2bRAD Genotyping Workshop at the USC Wrigley Marine Science Center. 2bRAD is a newly developed genetic technique used to genotype thousands of genetic loci simultaneously on the type IIB restriction endonuclease site and can be used without a reference genome. This method isolates tags on which single nucleotide polymorphisms (SNPs) can be identified and used for various applications in population dynamics and connectivity. The workshop was taught by the co-developer of the method, Eli Meyer from Oregon State University, and took place over 10 days.
Danielle brought 10 Montastraea cavernosa coral samples from the St. Lucie Reef project with her to the workshop where she successfully completed 2bRAD library preparation for later sequencing. This preliminary data will generate the SNP frequency for M. cavernosa and allow for initial comparison between the 2bRAD data and the microsatellite analysis for these same samples. She also prepared 10 oyster samples from the Meyer Lab to be sequenced and used for a group paper in collaboration with the other twelve workshop participants. After spending the first four days in the lab, the workshop participates moved into bioinformatics mode and had a crash course in command line interface, coding, and analysis of next-generation sequencing data for the remainder of the week. All participants successfully generated SNP loci for oyster samples previously sequenced and discussed further applications of 2bRAD data. Despite the long days in the molecular lab and coding, everyone was able to enjoy the beauty of the mountains and marine sanctuary on Catalina Island!
Danielle brought 10 Montastraea cavernosa coral samples from the St. Lucie Reef project with her to the workshop where she successfully completed 2bRAD library preparation for later sequencing. This preliminary data will generate the SNP frequency for M. cavernosa and allow for initial comparison between the 2bRAD data and the microsatellite analysis for these same samples. She also prepared 10 oyster samples from the Meyer Lab to be sequenced and used for a group paper in collaboration with the other twelve workshop participants. After spending the first four days in the lab, the workshop participates moved into bioinformatics mode and had a crash course in command line interface, coding, and analysis of next-generation sequencing data for the remainder of the week. All participants successfully generated SNP loci for oyster samples previously sequenced and discussed further applications of 2bRAD data. Despite the long days in the molecular lab and coding, everyone was able to enjoy the beauty of the mountains and marine sanctuary on Catalina Island!
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