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Title: Genome sequence of Frateuria aurantia type strain (Kondô 67T), a xanthomonade isolated from Lilium auratium Lindl.

Abstract

Frateuria aurantia (ex Kondô and Ameyama 1958) Swings et al. 1980 is a member of the bispecific genus Frateuria in the family Xanthomonadaceae, which is already heavily targeted for non-type strain genome sequencing. Strain Kondô 67T was initially (1958) identified as a member of ‘Acetobacter aurantius’, a name that was not considered for the approved list. Kondô 67T was therefore later designated as the type strain of the newly proposed acetogenic species Frateuria aurantia. The strain is of interest because of its triterpenoids (hopane family). F. aurantia Kondô 67T is the first member of the genus Frateura whose genome sequence has been deciphered, and here we describe the features of this organism, together with the complete genome sequence and annotation. The 3,603,458-bp long chromosome with its 3,200 protein-coding and 88 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.

Authors:
 [1];  [2];  [1];  [3];  [1];  [1];  [1];  [2];  [2];  [2];  [1];  [1];  [1];  [1];  [1];  [1];  [1];  [4];  [4];  [5] more »;  [6];  [7];  [2];  [7];  [1];  [1];  [8];  [4];  [9];  [1];  [7] « less
  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. St. Petersburg State Univ. (Russian Federation); St. Petersburg Academic Univ. (Russian Federation)
  4. Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
  5. Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
  6. Helmholtz Centre for Infection Research, Braunschweig (Germany)
  7. Leibniz Inst. DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig (Germany)
  8. USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); Univ. of California Davis Genome Center, CA (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 Lab. (LBNL), Berkeley, CA (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23); German Research Foundation (DFG); Russian Ministry of Science
OSTI Identifier:
1407204
Grant/Contract Number:  
AC02-05CH11231; AC52-07NA27344; AC02-06NA25396; AC05-00OR22725; INST 599/1-2; 11.G34.31.0068
Resource Type:
Accepted Manuscript
Journal Name:
Standards in Genomic Sciences
Additional Journal Information:
Journal Volume: 9; Journal ID: ISSN 1944-3277
Publisher:
BioMed Central
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; 60 APPLIED LIFE SCIENCES; strictly aerobic; motile; rod-shaped; acetogenic; mesophilic; Acetobacter aurantius; Xanthomonadaceae; GEBA

Citation Formats

Anderson, Iain, Teshima, Huzuki, Nolan, Matt, Lapidus, Alla, Tice, Hope, Del Rio, Tijana Glavina, Cheng, Jan-Fang, Han, Cliff, Tapia, Roxanne, Goodwin, Lynne A., Pitluck, Sam, Liolios, Konstantinos, Mavromatis, Konstantinos, Pagani, Ioanna, Ivanova, Natalia, Mikhailova, Natalia, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Rohde, Manfred, Lang, Elke, Detter, John C., Göker, Markus, Woyke, Tanja, Bristow, James, Eisen, Jonathan A., Markowitz, Victor, Hugenholtz, Philip, Kyrpides, Nikos C., and Klenk, Hans-Peter. Genome sequence of Frateuria aurantia type strain (Kondô 67T), a xanthomonade isolated from Lilium auratium Lindl.. United States: N. p., 2013. Web. doi:10.4056/sigs.4338002.
Anderson, Iain, Teshima, Huzuki, Nolan, Matt, Lapidus, Alla, Tice, Hope, Del Rio, Tijana Glavina, Cheng, Jan-Fang, Han, Cliff, Tapia, Roxanne, Goodwin, Lynne A., Pitluck, Sam, Liolios, Konstantinos, Mavromatis, Konstantinos, Pagani, Ioanna, Ivanova, Natalia, Mikhailova, Natalia, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Rohde, Manfred, Lang, Elke, Detter, John C., Göker, Markus, Woyke, Tanja, Bristow, James, Eisen, Jonathan A., Markowitz, Victor, Hugenholtz, Philip, Kyrpides, Nikos C., & Klenk, Hans-Peter. Genome sequence of Frateuria aurantia type strain (Kondô 67T), a xanthomonade isolated from Lilium auratium Lindl.. United States. doi:10.4056/sigs.4338002.
Anderson, Iain, Teshima, Huzuki, Nolan, Matt, Lapidus, Alla, Tice, Hope, Del Rio, Tijana Glavina, Cheng, Jan-Fang, Han, Cliff, Tapia, Roxanne, Goodwin, Lynne A., Pitluck, Sam, Liolios, Konstantinos, Mavromatis, Konstantinos, Pagani, Ioanna, Ivanova, Natalia, Mikhailova, Natalia, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Rohde, Manfred, Lang, Elke, Detter, John C., Göker, Markus, Woyke, Tanja, Bristow, James, Eisen, Jonathan A., Markowitz, Victor, Hugenholtz, Philip, Kyrpides, Nikos C., and Klenk, Hans-Peter. Wed . "Genome sequence of Frateuria aurantia type strain (Kondô 67T), a xanthomonade isolated from Lilium auratium Lindl.". United States. doi:10.4056/sigs.4338002. https://www.osti.gov/servlets/purl/1407204.
@article{osti_1407204,
title = {Genome sequence of Frateuria aurantia type strain (Kondô 67T), a xanthomonade isolated from Lilium auratium Lindl.},
author = {Anderson, Iain and Teshima, Huzuki and Nolan, Matt and Lapidus, Alla and Tice, Hope and Del Rio, Tijana Glavina and Cheng, Jan-Fang and Han, Cliff and Tapia, Roxanne and Goodwin, Lynne A. and Pitluck, Sam and Liolios, Konstantinos and Mavromatis, Konstantinos and Pagani, Ioanna and Ivanova, Natalia and Mikhailova, Natalia and Pati, Amrita and Chen, Amy and Palaniappan, Krishna and Land, Miriam and Rohde, Manfred and Lang, Elke and Detter, John C. and Göker, Markus and Woyke, Tanja and Bristow, James and Eisen, Jonathan A. and Markowitz, Victor and Hugenholtz, Philip and Kyrpides, Nikos C. and Klenk, Hans-Peter},
abstractNote = {Frateuria aurantia (ex Kondô and Ameyama 1958) Swings et al. 1980 is a member of the bispecific genus Frateuria in the family Xanthomonadaceae, which is already heavily targeted for non-type strain genome sequencing. Strain Kondô 67T was initially (1958) identified as a member of ‘Acetobacter aurantius’, a name that was not considered for the approved list. Kondô 67T was therefore later designated as the type strain of the newly proposed acetogenic species Frateuria aurantia. The strain is of interest because of its triterpenoids (hopane family). F. aurantia Kondô 67T is the first member of the genus Frateura whose genome sequence has been deciphered, and here we describe the features of this organism, together with the complete genome sequence and annotation. The 3,603,458-bp long chromosome with its 3,200 protein-coding and 88 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.},
doi = {10.4056/sigs.4338002},
journal = {Standards in Genomic Sciences},
number = ,
volume = 9,
place = {United States},
year = {2013},
month = {10}
}

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Works referenced in this record:

Frateuria, a New Genus for "Acetobacter aurantius"
journal, July 1980

  • Swings, J.; Gillis, M.; Kersters, K.
  • International Journal of Systematic Bacteriology, Vol. 30, Issue 3
  • DOI: 10.1099/00207713-30-3-547

Isolation and phylogenetic characterization of acidophilic microorganisms indigenous to acidic drainage waters at an abandoned Norwegian copper mine
journal, October 2001


Influence of the temperature and the growth phase on the hopanoids and fatty acids content of Frateuria aurantia (DSMZ 6220)
journal, March 2004


Basic local alignment search tool
journal, October 1990

  • Altschul, Stephen F.; Gish, Warren; Miller, Webb
  • Journal of Molecular Biology, Vol. 215, Issue 3, p. 403-410
  • DOI: 10.1016/S0022-2836(05)80360-2

Greengenes, a Chimera-Checked 16S rRNA Gene Database and Workbench Compatible with ARB
journal, July 2006

  • DeSantis, T. Z.; Hugenholtz, P.; Larsen, N.
  • Applied and Environmental Microbiology, Vol. 72, Issue 7, p. 5069-5072
  • DOI: 10.1128/AEM.03006-05

Multiple sequence alignment using partial order graphs
journal, March 2002


Selection of Conserved Blocks from Multiple Alignments for Their Use in Phylogenetic Analysis
journal, April 2000


A Rapid Bootstrap Algorithm for the RAxML Web Servers
journal, October 2008

  • Stamatakis, Alexandros; Hoover, Paul; Rougemont, Jacques
  • Systematic Biology, Vol. 57, Issue 5
  • DOI: 10.1080/10635150802429642

An empirical test of the midpoint rooting method: A TEST FOR THE MIDPOINT ROOTING METHOD
journal, December 2007


The Genomes OnLine Database (GOLD) v.4: status of genomic and metagenomic projects and their associated metadata
journal, December 2011

  • Pagani, I.; Liolios, K.; Jansson, J.
  • Nucleic Acids Research, Vol. 40, Issue D1
  • DOI: 10.1093/nar/gkr1100

The minimum information about a genome sequence (MIGS) specification
journal, May 2008

  • Field, Dawn; Garrity, George; Gray, Tanya
  • Nature Biotechnology, Vol. 26, Issue 5
  • DOI: 10.1038/nbt1360

The Genomic Standards Consortium
journal, June 2011


Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya.
journal, June 1990

  • Woese, C. R.; Kandler, O.; Wheelis, M. L.
  • Proceedings of the National Academy of Sciences, Vol. 87, Issue 12
  • DOI: 10.1073/pnas.87.12.4576

Frateuria terrea sp. nov., isolated from forest soil, and emended description of the genus Frateuria
journal, March 2010

  • Zhang, J. -Y.; Liu, X. -Y.; Liu, S. -J.
  • INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Vol. 61, Issue 2
  • DOI: 10.1099/ijs.0.021618-0

Carbohydrate Metabolism by Acetobacter Species
journal, January 1958

  • KondÔ, Keiji; Ameyama, Minoru
  • Bulletin of the Agricultural Chemical Society of Japan, Vol. 22, Issue 6
  • DOI: 10.1271/bbb1924.22.369

Gene Ontology: tool for the unification of biology
journal, May 2000

  • Ashburner, Michael; Ball, Catherine A.; Blake, Judith A.
  • Nature Genetics, Vol. 25, Issue 1
  • DOI: 10.1038/75556

Isolation and Characterization of "Polarly Flagellated Intermediate Strains" in Acetic acid Bacteria
journal, January 1976

  • Yamada, Yuzo; Okada, Yoshito; Kondo, Keiji
  • The Journal of General and Applied Microbiology, Vol. 22, Issue 5
  • DOI: 10.2323/jgam.22.237

En route to a genome-based classification of Archaea and Bacteria?
journal, June 2010


A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea
journal, December 2009

  • Wu, Dongying; Hugenholtz, Philip; Mavromatis, Konstantinos
  • Nature, Vol. 462, Issue 7276
  • DOI: 10.1038/nature08656

The Fast Changing Landscape of Sequencing Technologies and Their Impact on Microbial Genome Assemblies and Annotation
journal, December 2012


The DNA Bank Network: The Start from a German Initiative
journal, March 2011

  • Gemeinholzer, Birgit; Dröge, Gabriele; Zetzsche, Holger
  • Biopreservation and Biobanking, Vol. 9, Issue 1
  • DOI: 10.1089/bio.2010.0029

Velvet: Algorithms for de novo short read assembly using de Bruijn graphs
journal, February 2008


Prodigal: prokaryotic gene recognition and translation initiation site identification
journal, March 2010


The DOE-JGI Standard Operating Procedure for the Annotations of Microbial Genomes
journal, July 2009

  • Mavromatis, Konstantinos; Ivanova, Natalia N.; Chen, I-Min A.
  • Standards in Genomic Sciences, Vol. 1, Issue 1
  • DOI: 10.4056/sigs.632

GenePRIMP: a gene prediction improvement pipeline for prokaryotic genomes
journal, May 2010

  • Pati, Amrita; Ivanova, Natalia N.; Mikhailova, Natalia
  • Nature Methods, Vol. 7, Issue 6
  • DOI: 10.1038/nmeth.1457

IMG ER: a system for microbial genome annotation expert review and curation
journal, June 2009