Dataset: Candidatus Thioglobus singularis strain PS1
Deployment: TN268

Complete genome sequence - first cultured mixotroph from SUP05 clade

View Data: For data, See Dataset Metadata Page: https://www.bco-dmo.org/dataset/628767

Principal Investigator:

Robert Morris (University of Washington, UW)

Contact:

Robert Morris (University of Washington, UW)

BCO-DMO Data Manager:

Ms Dicky Allison (Woods Hole Oceanographic Institution, WHOI BCO-DMO)

Project:

Mixotrophic bacteria and the cryptic marine sulfur cycle: Mechanisms of carbon assimilation and sulfur oxidation in the Arctic96BD-19 GSO clade (Sulfur Oxidizers)

Current State:

Preliminary and in progress

Version:

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Description

The complete genome sequence of Candidatus Thioglobus singularis strain PS1, the first cultured mixotrophic representative from the SUP05 clade.

See Announcement.

N.B.: In bacterial nomenclature, Candidatus is a component of the taxonomic name for a bacterium that cannot be maintained in a bacteriology culture collection. Candidatus status may be used when a species or genus is well characterized but yet-uncultured. (Murray and Schleifer, 1994) With today's technology much information is obtained by 16S ribosomal RNA or even near-complete genomes with modern metagenomics techniques. [paraphrased from Wikipedia]

Methods & Sampling

Dataset acquisition description

Cultures of T. singularis were grown in one-liter polycarbonate bottles of filter sterilized seawater media as described in Marshall and Morris, 2012. . Cells were then filtered onto sterile 0.2 µm polyethersulfone filters (Pall, Port Washington, NY), placed in 15 mL Teflon tubes containing 2 ml of sucrose lysis buffer (SLB), and flash frozen in liquid nitrogen. Cells were later lysed by adding 100 µL of 1mg/mL lysozyme and incubating at 4 °C for 60 minutes, then by adding 465 µL of 10% SDS and 250 µL of proteinase K and incubating at 55 °C for 2 hours. DNA was extracted and purified from cell lysates using DNeasy Blood and Tissue and Minelute kits according the manufacturers instructions, respectively (QIAGEN, Germantown, MD). A total of 20.35 µg of DNA was used to construct a mate pair library according to the SOLiD™v3.0 mate-pair protocol (Life Technologies, Foster City, CA).

Data Processing Description

Dataset Processing Description

The T. singularis genome was assembled using SEAStAR v. 0.4.17 as described in Iverson et al (2012). The initial assembly was 97% complete and contained 177 gaps with a mean gap length of 198 bp. Gaps were closed by PCR with custom primers designed using Geneious 7.0.4 (Biomatters, Auckland, NZ). Amplification products were visualized, gel purified, and sequenced by Genewiz (Foster City, CA). The complete genome sequence (1,714,148bp) was confirmed by performing additional PCR reactions to resolve any irregularities in the assembly and by comparing read coverage, physical coverage and insert sizes of mate pairs covering the genome. Annotations were performed using the NCBI Prokaryotic Genome Automatic Annotation Pipeline and were checked against RAST annotations, IMG annotations , and in some cases by phylogenetic analyses. Discrepancies were corrected and final annotations were submitted to NCBI.

More information about this dataset deployment

Funding

Award Number	Funding Source
OCE-1232840	NSF Division of Ocean Sciences

Instruments

None available yet

Parameters

Supplied Name	Supplied description	Supplied Units	Standard Name
entry	name of bacteria	text	sample
GenBank_accession	link to NCBI GenBank	link	accession_number
lat	Latitude	decimal degrees	lat
lon	Longitude; West is negative	decimal degrees	lon
depth	Sampling depth	meters	depth
month	month sampling took place	text	month_local
year	year sampling took place	number	year
description	name of GenBank file with complete genome	text	brief_desc

Database

Contribute Data

Dataset: Candidatus Thioglobus singularis strain PS1
Deployment: TN268

Dataset acquisition description

Dataset Processing Description

Database

Contribute Data

Dataset: Candidatus Thioglobus singularis strain PS1Deployment: TN268

Dataset acquisition description

Dataset Processing Description

Dataset: Candidatus Thioglobus singularis strain PS1
Deployment: TN268