Dataset: Eukaryotic viruses encode the ribosomal protein eL40

Name: NCBI accession metadata for Eukaryotic viruses encoding ribosomal protein eL40 from samples collected on KM1419 and KM1108 from Mar 2011 to Sep 2014
Published: 2025-01-22
Keywords: Nucleocytoviricota, giant virus, dictyochophyte, rhodopsin, phytoplankton, biota, oceans

View Data: Data not available yet

Cite This Dataset

Spatial Extent: N:22.90065 E:-157.886274 S:21.246098 W:-159.107376

Pacific Ocean North waters, Station ALOHA, 22°45’ N, 158°00’ W depth 25m and 45m

Temporal Extent: 2011-03-27 - 2014-09-17

Project:

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

Principal Investigator:

Kyle F. Edwards (University of Hawaiʻi at Mānoa)

Grieg Steward (University of Hawaiʻi at Mānoa)

Scientist:

Christopher Schvarcz (University of Hawaiʻi at Mānoa)

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, WHOI BCO-DMO)

Version:

Version Date:

2025-01-22

Restricted:

Validated:

Current State:

Preliminary and in progress

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

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 features of the genome, including the encoding of a ribosomal protein (eL40) and a group II viral rhodopsin. The research explores the affiliations and possible origins of these genes, supported by metagenomic and metatranscriptomic data indicating the presence and expression of eL40 in other giant viruses. This study expands the understanding of the metabolic versatility of eukaryoviruses and proposes new mechanisms by which these viruses can manipulate host resources and energy.

Expand/Collapse All

Methods & Sampling

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.

Data Processing Description

The FloV-SA2 genome was assembled from PacBio sequencing reads using Canu v1.0 and polished using a combination of pbalign v0.2.0.141024 and Quiver v2.0.0.

Initial gene prediction was conducted with Prokka v1.14.5. Functional annotations were performed using a BLASTp search using Diamond (v2.1.4) against:

*NCBI Refseq databases (O’Leary et al., 2015)

*InterProScan (Jones et al., 2014)

BCO-DMO Processing

-imported "Data-samples-info-V2-2024-10-15.xlsx" into the BCO-DMO data system
-split column containing lat and lon
-converted lon to negative to represent decimal degrees
-converted date to YYYY-mm-dd
-renamed fields to conform with BCO-DMO naming conventions
-exported file as "949101_v1_eukaryotic_viruses_flov-sa2.csv"

More Information about this dataset

Funding Sources

Funding Source	Award Number
NSF Division of Ocean Sciences	OCE-2129697
NSF Office of Integrative Activities	OIA-1736030
Simons Foundation	566853

Deployments

Deployment	Synonyms	Start Date	Platform	Investigator
KM1108	HOT-230	2011-02-27	R/V Kilo Moana	Susan E. Curless (Chief Scientist)	data info
KM1419	HOT-265	2014-09-13	R/V Kilo Moana	Fernando Santiago-Mandujano (Chief Scientist)	data info

Instruments

Automated DNA Sequencer

Supplied Name: Illumina (NextSeq System)

Supplied Description:

DNA was sequenced using Illumina (NextSeq System) and PacBio methods.

Instrument Type

Generic Name: Automated DNA Sequencer

Acronym: Automated Sequencer

Generic Description:

General term for a laboratory instrument used for deciphering the order of bases in a strand of DNA. Sanger sequencers detect fluorescence from different dyes that are used to identify the A, C, G, and T extension reactions. Contemporary or Pyrosequencer methods are based on detecting the activity of DNA polymerase (a DNA synthesizing enzyme) with another chemoluminescent enzyme. Essentially, the method allows sequencing of a single strand of DNA by synthesizing the complementary strand along it, one base pair at a time, and detecting which base was actually added at each step.

Automated DNA Sequencer

Supplied Name: PacBio

Supplied Description:

DNA was sequenced using Illumina (NextSeq System) and PacBio methods.

Instrument Type

Generic Name: Automated DNA Sequencer

Acronym: Automated Sequencer

Generic Description:

Centrifuge

Supplied Name: centrifugal ultrafiltration

Supplied Description:

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.

Instrument Type

Generic Name: Centrifuge

Generic Description:

A machine with a rapidly rotating container that applies centrifugal force to its contents, typically to separate fluids of different densities (e.g., cream from milk) or liquids from solids.

Thermal Cycler

Supplied Name: PCR

Supplied Description:

Florenciella 18S rRNA was amplified by PCR then cloned and extracted using the Zyppy Plasmid Miniprep Kit (Zymo Research).

Instrument Type

Generic Name: Thermal Cycler

Generic Description:

A thermal cycler or "thermocycler" is a general term for a type of laboratory apparatus, commonly used for performing polymerase chain reaction (PCR), that is capable of repeatedly altering and maintaining specific temperatures for defined periods of time. The device has a thermal block with holes where tubes with the PCR reaction mixtures can be inserted. The cycler then raises and lowers the temperature of the block in discrete, pre-programmed steps. They can also be used to facilitate other temperature-sensitive reactions, including restriction enzyme digestion or rapid diagnostics.

(adapted from http://serc.carleton.edu/microbelife/research_methods/genomics/pcr.html)

Parameters

Date and time formats are described in python strftime() syntax.

Supplied Name	Supplied description	Supplied Units	Standard Name
Taxa_name	Taxa name of genome of FloV-SA2 (phylum Nucleocytoviricota) and Florenciella sp.strain UHM3020	units	taxon
Source_of_sample	Source of sample used for derived genome	units	sample_type
Genbank_accession	Genbank assession number associated with FloV-SA2 and Florenciella sp.strain UHM3020	units	accession_number
Bioproject_number	Bioproject number associated with FloV-SA2 and Florenciella sp.strain UHM3020	units	BioProject
Latitude	Latitude for sample collection in decimal degrees, postive values are North	units	lat
Longitude	Coordinates for sample collection in decimal degrees, postive values are East	units	lon
Date_Isolated	Date genome was isolated from Pacific ocean at Station Aloha in Marine Viral Ecology Laboratories Format: %Y-%m-%d	units	date

Status message

Database

Contribute Data

Dataset: Eukaryotic viruses encode the ribosomal protein eL40