Dataset: Eukaryotic viruses encode the ribosomal protein eL40
Deployment: KM1108

Note: The detailed protocols are described in Thomy et al., 2024

For eukaryote isolation, seawater sampling was carried out on March 02, 2011 from the oligotrophic open-ocean site at Station ALOHA, in the North Pacific Subtropical Gyre at a depth of 45 meters. Seawater samples were enriched with Keller (K) medium and unialgal cultures were then isolated by serial dilution to extinction. Florenciella sp. strain UHM3020 was further identified by small subunit ribosomal RNA gene (18S rRNA gene) sequencing. DNA was extracted from the pellets using the MasterPure Complete DNA and RNA Purification Kit (Epicentre). Florenciella 18S rRNA was amplified by PCR then cloned and extracted using the Zyppy Plasmid Miniprep Kit (Zymo Research). Near-full-length 18S rRNA gene for Florenciella was sequenced using Sanger method.

For virus isolation, seawater sampling was carried out on September 15, 2014 from the same site as described previously for the host isolation at a depth of 25 meters. Forty liters of seawater was filtered through 0.8 μm pore size filters to remove larger cells while minimizing losses of large viruses. Viral particles in the filtrate were concentrated by tangential flow filtration (TFF; 30 kDA molecular weight cut-off). The concentrate was amended with nutrients to match K medium and then used to challenge a culture of a healthy Florenciella culture isolated previously from the same water. Viruses in the filtrate were concentrated by TFF (30 kDa) to 300 mL volume, further concentrated to 0.5 mL by centrifugal ultrafiltration (30 kDa) and then purified in a CsCl buoyant density gradient. DNA was extracted from the virus peak in the gradient using Masterpure Complete DNA and RNA Purification Kit (LGC Biosearch Technologies). DNA was sequenced using Illumina (NextSeq System) and PacBio methods.

The FloV-SA2 complete genome sequence was deposited in GenBank with accession number PP542043 (see related datasets) as well as the ubiquitin-60S ribosomal protein eL40 gene sequence encoded in the Florenciella sp. host genome PP665604 (see related datasets). The gene annotations were published as Supplementary Table 1 in Thomy et al., 2024.