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Title: Genome sequence of the filamentous, gliding Thiothrix nivea neotype strain (JP2T)

Abstract

Thiothrix nivea (Rabenhorst 1865) Winogradsky 1888 (Approved Lists 1980) emend. Larkin and Shinabarger 1983 is the type species of the genus Thiothrix in the family Thiotrichaceae. The species is of interest not only because of its isolated location in the yet to be genomically characterized region of the tree of life, but also because of its life-style with gliding gonidia, the multilayer sheath, rosettes, and the embedded sulfur granules. Strain JP2T is the neotype strain of the species which was first observed by Rabenhorst in 1865 and later reclassified by Winogradsky in 1888 into the then novel genus Thiothrix. This is the first completed (improved-high-quality-draft) genome sequence to be published of a member of the family Thiotrichaceae. The genome in its current assembly consists of 15 contigs in four scaffolds with a total of 4,691,711 bp bearing 4,542 protein-coding and 52 RNA genes and is a part of the Genomic Encyclopedia of Bacteria and Archaea project.

Authors:
 [1];  [1];  [1];  [1];  [1];  [1];  [2];  [2];  [2];  [1];  [1];  [1];  [1];  [1];  [1];  [1];  [1];  [3];  [3];  [4] more »;  [5];  [6];  [5];  [5];  [5];  [1];  [7];  [8];  [9];  [1];  [5];  [1] « less
+ Show Author Affiliations
  1. USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
  2. USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); Los Alamos National Lab. (LANL), Los Alamos, NM (United States)
  3. Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
  4. USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
  5. German Collection of Microorganisms and Cell Cultures, Braunschweig (Germany)
  6. Helmholtz Centre for Infection Research, Braunschweig (Germany)
  7. USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); Univ. of California, Davis, CA (United States)
  8. Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
  9. USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); Univ. of Queensland, Brisbane, QLD (Australia)
Publication Date:
Research Org.:
Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Biological and Environmental Research (BER); German Research Foundation (DFG)
OSTI Identifier:
1630579
Grant/Contract Number:  
AC02-05CH11231; AC52-07NA27344; AC02-06NA25396; AC05-00OR22725; INST 599/1-1
Resource Type:
Accepted Manuscript
Journal Name:
Standards in Genomic Sciences
Additional Journal Information:
Journal Volume: 5; Journal Issue: 3; Journal ID: ISSN 1944-3277
Publisher:
BioMed Central
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; strictly aerobic; gliding motility; Gram-negative; mesophile; sheath; filaments; sulfur granules; Thiotrichaceae; GEBA

Citation Formats

Lapidus, Alla, Nolan, Matt, Lucas, Susan, Glavina Del Rio, Tijana, Tice, Hope, Cheng, Jan-Fang, Tapia, Roxanne, Han, Cliff, Goodwin, Lynne, Pitluck, Sam, Liolios, Konstantinos, Pagani, Ioanna, Ivanova, Natalia, Huntemann, Marcel, Mavromatis, Konstantinos, Mikhailova, Natalia, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Brambilla, Evelyne-Marie, Rohde, Manfred, Abt, Birte, Verbarg, Susanne, Göker, Markus, Bristow, James, Eisen, Jonathan A., Markowitz, Victor, Hugenholtz, Philip, Kyrpides, Nikos C., Klenk, Hans-Peter, and Woyke, Tanja. Genome sequence of the filamentous, gliding Thiothrix nivea neotype strain (JP2T). United States: N. p., 2011. Web. doi:10.4056/sigs.2344929.
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Lapidus, Alla, Nolan, Matt, Lucas, Susan, Glavina Del Rio, Tijana, Tice, Hope, Cheng, Jan-Fang, Tapia, Roxanne, Han, Cliff, Goodwin, Lynne, Pitluck, Sam, Liolios, Konstantinos, Pagani, Ioanna, Ivanova, Natalia, Huntemann, Marcel, Mavromatis, Konstantinos, Mikhailova, Natalia, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Brambilla, Evelyne-Marie, Rohde, Manfred, Abt, Birte, Verbarg, Susanne, Göker, Markus, Bristow, James, Eisen, Jonathan A., Markowitz, Victor, Hugenholtz, Philip, Kyrpides, Nikos C., Klenk, Hans-Peter, & Woyke, Tanja. Genome sequence of the filamentous, gliding Thiothrix nivea neotype strain (JP2T). United States. https://doi.org/10.4056/sigs.2344929
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Lapidus, Alla, Nolan, Matt, Lucas, Susan, Glavina Del Rio, Tijana, Tice, Hope, Cheng, Jan-Fang, Tapia, Roxanne, Han, Cliff, Goodwin, Lynne, Pitluck, Sam, Liolios, Konstantinos, Pagani, Ioanna, Ivanova, Natalia, Huntemann, Marcel, Mavromatis, Konstantinos, Mikhailova, Natalia, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Brambilla, Evelyne-Marie, Rohde, Manfred, Abt, Birte, Verbarg, Susanne, Göker, Markus, Bristow, James, Eisen, Jonathan A., Markowitz, Victor, Hugenholtz, Philip, Kyrpides, Nikos C., Klenk, Hans-Peter, and Woyke, Tanja. Sat . "Genome sequence of the filamentous, gliding Thiothrix nivea neotype strain (JP2T)". United States. https://doi.org/10.4056/sigs.2344929. https://www.osti.gov/servlets/purl/1630579.
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@article{osti_1630579,
title = {Genome sequence of the filamentous, gliding Thiothrix nivea neotype strain (JP2T)},
author = {Lapidus, Alla and Nolan, Matt and Lucas, Susan and Glavina Del Rio, Tijana and Tice, Hope and Cheng, Jan-Fang and Tapia, Roxanne and Han, Cliff and Goodwin, Lynne and Pitluck, Sam and Liolios, Konstantinos and Pagani, Ioanna and Ivanova, Natalia and Huntemann, Marcel and Mavromatis, Konstantinos and Mikhailova, Natalia and Pati, Amrita and Chen, Amy and Palaniappan, Krishna and Land, Miriam and Brambilla, Evelyne-Marie and Rohde, Manfred and Abt, Birte and Verbarg, Susanne and Göker, Markus and Bristow, James and Eisen, Jonathan A. and Markowitz, Victor and Hugenholtz, Philip and Kyrpides, Nikos C. and Klenk, Hans-Peter and Woyke, Tanja},
abstractNote = {Thiothrix nivea (Rabenhorst 1865) Winogradsky 1888 (Approved Lists 1980) emend. Larkin and Shinabarger 1983 is the type species of the genus Thiothrix in the family Thiotrichaceae. The species is of interest not only because of its isolated location in the yet to be genomically characterized region of the tree of life, but also because of its life-style with gliding gonidia, the multilayer sheath, rosettes, and the embedded sulfur granules. Strain JP2T is the neotype strain of the species which was first observed by Rabenhorst in 1865 and later reclassified by Winogradsky in 1888 into the then novel genus Thiothrix. This is the first completed (improved-high-quality-draft) genome sequence to be published of a member of the family Thiotrichaceae. The genome in its current assembly consists of 15 contigs in four scaffolds with a total of 4,691,711 bp bearing 4,542 protein-coding and 52 RNA genes and is a part of the Genomic Encyclopedia of Bacteria and Archaea project.},
doi = {10.4056/sigs.2344929},
journal = {Standards in Genomic Sciences},
number = 3,
volume = 5,
place = {United States},
year = {Sat Dec 31 00:00:00 EST 2011},
month = {Sat Dec 31 00:00:00 EST 2011}
}
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Journal Article:
Free Publicly Available Full Text
Publisher's Version of Record
https://doi.org/10.4056/sigs.2344929
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Cited by: 11 works
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Figures / Tables:

Figure 1 Figure 1: Phylogenetic tree highlighting the position of T. nivea relative to the other type strains within the family Thiotrichaceae. The tree was inferred from 1,332 aligned characters of the 16S rRNA gene sequence under the maximum likelihood (ML) criterion. Rooting was done initially using the midpoint method and thenmore » checked for its agreement with the current classification (Table 1). The branches are scaled in terms of the expected number of substitutions per site. Numbers adjacent to the branches are support values from 200 ML bootstrap replicates (left) and from 1,000 maximum parsimony bootstrap replicates (right) if larger than 60%. Lineages with type strain genome sequencing projects registered in GOLD are labeled with one asterisk, those also listed as 'Complete and Published' with two asterisks.« less
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