Dataset: NCBI accession metadata for Eukaryotic viruses encoding ribosomal protein eL40 from samples collected on KM1419 and KM1108 from Mar 2011 to Sep 2014

ValidatedFinal no updates expectedDOI: 10.26008/1912/bco-dmo.949101.1Version 1 (2025-01-22)Dataset Type:Cruise Results

Principal Investigator: Kyle F. Edwards (University of Hawaiʻi at Mānoa)

Principal Investigator: Grieg Steward (University of Hawaiʻi at Mānoa)

Scientist: Christopher Schvarcz (University of Hawaiʻi at Mānoa)

Scientist: Julie Thomy (University of Hawaiʻi at Mānoa)

Technician: Kelsey McBeain (University of Hawaiʻi at Mānoa)

BCO-DMO Data Manager: Audrey Mickle (Woods Hole Oceanographic Institution)


Project: Giant viruses in the open ocean: Is large size adaptive where cells are scarce? (GVs NPSG)


Abstract

This dataset contains sample collection metadata, as well as GenBank accessions and relevant Bioproject numbers for FloV-SA2 samples collected on KM1419 and KM1108 at Station ALOHA from Mar 2011 to Sep 2014. This study analyzes the genome of FloV-SA2 (phylum Nucleocytoviricota), a cultured marine virus isolated from open ocean seawater in the Pacific Ocean using a marine microalga strain (UHM3020) in the genus Florenciella (class Dictyochophyceae) as a host. The analysis highlights unique fe...

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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.


Related Datasets

References

Dataset: https://www.ncbi.nlm.nih.gov/nuccore/PP665604
Thomy,J., Schvarcz,C.R., McBeain,K.A., Edwards,K.F. and Steward,G.F. (2024). Florenciella sp. strain UHM3020 ubiquitin-60S ribosomal protein eL40 gene, complete cds. GenBank accession number PP665604 [GenBank]. https://www.ncbi.nlm.nih.gov/nuccore/PP665604
References

Dataset: https://www.ncbi.nlm.nih.gov/nuccore/PP542043
Thomy,J., Schvarcz,C.R., McBeain,K.A., Edwards,K.F. and Steward,G.F. (2024). Florenciella sp. virus SA2 isolate FloV-SA2, complete genome. GenBank accession number PP542043. [GenBank]. https://www.ncbi.nlm.nih.gov/nuccore/PP542043
References

Dataset: http://www.ncbi.nlm.nih.gov/bioproject/PRJNA1169929
University of Hawaii. Florenciella sp. UHM3020, Florenciella sp.strain UHM3020. 2024/10. In: BioProject [Internet]. Bethesda, MD: National Library of Medicine (US), National Center for Biotechnology Information; 2011-. Available from: http://www.ncbi.nlm.nih.gov/bioproject/PRJNA1169929. NCBI:BioProject: PRJNA1169929.
References

Dataset: http://www.ncbi.nlm.nih.gov/bioproject/PRJNA1169927
University of Hawaii. Florenciella sp. virus SA2 isolate genome sequencing. 2024/10. In: BioProject [Internet]. Bethesda, MD: National Library of Medicine (US), National Center for Biotechnology Information; 2011-. Available from: http://www.ncbi.nlm.nih.gov/bioproject/PRJNA1169927. NCBI:BioProject: PRJNA1169927.

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