Environmental Genomics of Salpa thompsoni in the Southern Ocean

Salpa thompsoni samples were collected during two cruises in the Southern Ocean in 2009 and 2010. Individual salp specimens were identified while alive, dissected to remove the gut and gut contents, and flash-frozen individually in liquid nitrogen or preserved in 95% ethanol for molecular genetic and genomic analysis. Salpa thompsoni – the target species for this SGER award and the focus of this research – was selected as a 454 sequencing facility pilot project. This included whole-genome library preparation by shotgun and paired-end pyrosequencing, data analysis and bioinformatics, and presentation of results. Genomic DNA was amplified by emPCR; pyrosequencing was carried out on the amplified fragments. Sequences were aligned and assembled into contigs (i.e., DNA sequences) and scaffolds with GsAssembler software from Roche. Preliminary sequence analysis was done using Blast2GO (http://www.blast2go.de), a tool for annotation, visualization, and functional genomic analysis.