Dataset: NCBI accession numbers for S. arcuata and S. meunieri

Name: NCBI accession numbers from a study of two tintinnid ciliate species, Schmidingerella arcuata and Schmidingerella meunieri
Published: 2024-06-13
Keywords: ciliate, genome, transcriptomes, oceans

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Cite This Dataset

Spatial Extent: N:48.5 E:-72.06 S:41.31 W:-122.7

Northwest Atlantic continental shelf (New England coast) and Puget Sound

Temporal Extent: 2019 - 2019

Project:

Collaborative Research: Combining single-cell and community 'omics' to test hypotheses about diversity and function of planktonic ciliates (Ciliate Omics)

Principal Investigator:

George McManus (University of Connecticut, UConn)

Co-Principal Investigator:

Laura A. Katz (Smith College)

Luciana Santoferrara (Hofstra University)

BCO-DMO Data Manager:

Shannon Rauch (Woods Hole Oceanographic Institution, WHOI BCO-DMO)

Version:

Version Date:

2024-06-13

Restricted:

Validated:

Current State:

Data not available

NCBI accession numbers from a study of two tintinnid ciliate species, Schmidingerella arcuata and Schmidingerella meunieri

Abstract:

Many ciliates express their genes only after "unscrambling" them from the genome (portions of the gene may be reversed in the genome or expressed in a different order from what is in the genome). Because the scrambling process would have to be unique to a given species, we can use genome/transcriptome comparisons of single cells to define species boundaries. We showed that two tintinnid ciliate species that look almost identical, Schmidingerella arcuata and S. meunieri, scramble and unscramble their genes differently in the step before transcription, verifying that they represent two distinct biological species. We are also using the single-cell -omics data to better understand the evolutionary relationships (phylogenomics) among tintinnids and related planktonic ciliates. The information in this dataset indicates how to access the sequence data from NCBI.

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Methods & Sampling

This project required sequencing whole genomes and transcriptomes from single cells picked from two cultures. One was Schmidingerella arcuata (urn:lsid:marinespecies.org:taxname:732664), isolated from the East Coast of the United States in Long Island Sound; the other was Schmidingerella meunieri (urn:lsid:marinespecies.org:taxname:732864), isolated by S. Strom from Puget Sound on the West Coast of the United States. S. arcuata was collected from the surface waters of northeastern Long Island Sound, CT (41.31°N, 72.06°W), using a 20-micrometer (µm) mesh plankton net. Single cells were isolated with drawn capillaries and moved to six-well culture plates with 0.2-µm-filtered sample water. The goal was to quantify the degree of difference in genome architecture for these two close congeners.

The cultures were grown in filtered seawater at 18 degrees Celsius (°C) on a 12:12 light cycle and fed the dinoflagellate Heterocapsa triquetra and the prymnesiophyte Isochrysis galbana. Individual cells were picked with a drawn capillary pipette and processed for sequencing as detailed below (from Smith et al 2020).

The SMART-Seq2 v4 Ultra Low input RNA kit (Cat: 634889; Takara, Mountain View, CA) was used for whole transcriptome amplification (WTA) following the manufacturer's protocols, with the exception that we quartered the reaction volumes. For whole-genome amplification (WGA), the Repli-g single-cell kit (Cat: 150343; Qiagen, Hilden, Germany) was used following the manufacturer’s protocols. The products (cDNA for WTA, gDNA for WGA) were quantified with the dsDNA Qubit assay (Invitrogen, Waltham, MA) and polymerase chain reaction-checked with eukaryotic 18S rDNA and genus-specific ITS primers. Minimum bacterial contamination was confirmed by polymerase chain reaction with 16S rDNA primers Sequencing libraries were prepared with the Illumina Nextera XT kit (Cat: FC1311096; Illumina, San Diego, CA), then processed with Illumina HiSeq 2500 at Macrogen Sequencing (Geumcheon-gu, Seoul, South Korea).

The isolation/cultivation was done in 2014-2015. The sequencing work was all completed and analyzed by the suummer of 2020.

Data Processing Description

Raw reads from WTA and WGA sequencing were trimmed for quality and size (Q28 and minimum length of 200 and 1,500 bp, respectively) using BBMap (V38.39). After trimming, two single-cell WTAs were assembled together using rnaSPAdes (V3.13.1), and seven singe-cell WGAs were assembled together using both SPAdes (V3.13.1) and MEGAHIT (V1.2.9). The MEGAHIT genome assembly was used for the final analysis.

Assemblies were processed through custom python scripts (https://github.com/maurerax/KatzLab/tree/HTS-Processing-PhyloGenPipeline) for the removal of rDNA and prokaryotic transcripts, and for the identification of orthologous gene families using USEARCH (V9.2) with OrthoMCLdatabases (V2.0.9).

BCO-DMO Processing

- Imported original file "NCBI_data_Schmidingerella.csv" into the BCO-DMO system.
- Removed "N" and "W" from the latitude and longitude columns.
- Made longitude negative to indicate the west direction.
- Renamed fields to comply with BCO-DMO naming conventions.
- Saved the final file as "924260_v1_ncbi_accessions.csv"

More Information about this dataset

Funding Sources

Funding Source	Award Number
NSF Division of Ocean Sciences	OCE-1924527
NSF Division of Ocean Sciences	OCE-1924570

Deployments

None available yet

Instruments

Automated DNA Sequencer

Supplied Name: Illumina HiSeq 2500

Supplied Description:

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.

Phytoplankton Net

Supplied Name: 20-µm-mesh plankton net

Supplied Description:

Instrument Type

Generic Name: Phytoplankton Net

Community Identifier: http://vocab.nerc.ac.uk/collection/L05/current/22/

Generic Description:

A Phytoplankton Net is a generic term for a sampling net having mesh size of 150 microns or less that is used to collect phytoplankton. It is used only when detailed instrument documentation is not available.

Parameters

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

Supplied Name	Supplied description	Supplied Units	Standard Name
species	Scientific name (Genus species) or "primer"	unitless	species
latitude	latitude of location from which species was isolated; positive values = North	decimal degrees	lat
longitude	longitude of location from which species was isolated; negative values = West	decimal degrees	lon
depth	depth from which ciliate was isolated	meters	depth
date	year of ciliate isolation Format: %Y	unitless	year
NCBI_BioprojectProject_ID	NCBI BioProject identifier	unitless	BioProject
Sample_Accession	NCBI BioSample identifier	unitless	BioSample
Sequence_Accession	Accession numbers at NCBI (sample or sequence) (Genbank or SRA database)	unitless	accession_number
sample	sequence locus or library type	unitless	sample_descrip
other_links	web links to data illustrations on figshare website	unitless	external_link

Status message

Database

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Dataset: NCBI accession numbers for S. arcuata and S. meunieri