Genomes of single stranded DNA viruses identified in a fecal sample of south polar skua (Stercorarius maccormicki) in the Antarctica
Approximately 5 g of the fecal sample was resuspended in 20 ml of SM buffer (0.1 M NaCl, 50mM Tris/HClpH 7.4, 10mM MgSO4), homogenized by vertexing and centrifuged at 10,000 g for 10 min. The supernatant was sequentially filtered through 0.45 and 0.2 m (pore size) syringe filter and the viral particles in the filtrate were precipitated with 15% w/v PEG 8000. The resulting solution was centrifuged at 6000g for 20 min and the pellet was resuspended in 2ml of SM buffer. Of this 200 l was used to extract viral DNA using the High Pure Viral Nucleic Acid Kit (Roche Diagnostics) and the circular DNA in this extract was enriched by rolling-circle amplification (RCA) using the TempliPhiTM kit (GE Healthcare). The RCA products were used to generate 90-bp paired-end library at BGI Hong Kong and sequenced on their Illumina 2500 sequencer.