Draft Genome Sequence of an Oscillatorian Cyanobacterium, Strain ESFC-1

Everroad, R. C.; Woebken, D.; Singer, S. W.; Burow, L. C.; Kyrpides, N.; Woyke, T.; Goodwin, L.; Detweiler, A.; Prufert-Bebout, L.; Pett-Ridge, J.

doi:10.1128/genomeA.00527-13

Title: Draft Genome Sequence of an Oscillatorian Cyanobacterium, Strain ESFC-1

Abstract

The nonheterocystous filamentous cyanobacterium strain ESFC-1 has recently been isolated from a marine microbial mat system, where it was identified as belonging to a recently discovered lineage of active nitrogen-fixing microorganisms. Here, we report the draft genome sequence of this isolate. The assembly consists of 3 scaffolds and contains 5,632,035 bp with a GC content of 46.5%.

Authors:

Everroad, R. C. ^[1]; Woebken, D. ^[2]; Singer, S. W. ^[3]; Burow, L. C. ^[2]; Kyrpides, N. ^[4]; Woyke, T. ^[4]; Goodwin, L. ^[5]; Detweiler, A. ^[1]; Prufert-Bebout, L. ^[1]; Pett-Ridge, J. ^[6]

NASA Ames Research Center (ARC), Moffett Field, Mountain View, CA (United States). Exobiology Branch
NASA Ames Research Center (ARC), Moffett Field, Mountain View, CA (United States). Exobiology Branch; Stanford Univ., CA (United States). Dept. of Chemical Engineering. Dept. of Civil and Environmental Engineering
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Earth Sciences Division
USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
Los Alamos National Lab. (LANL), Los Alamos, NM (United States)
Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States). Physical and Life Sciences Directorate

Publication Date:: Thu Aug 01 00:00:00 EDT 2013

Research Org.:: Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)

Sponsoring Org.:: USDOE Office of Science (SC), Biological and Environmental Research (BER)

OSTI Identifier:: 1524730

Report Number(s):: LLNL-JRNL-639128
Journal ID: ISSN 2169-8287; 758339

Grant/Contract Number:: AC52-07NA27344; AC02-05CH11231

Resource Type:: Accepted Manuscript

Journal Name:: Genome Announcements

Additional Journal Information:: Journal Volume: 1; Journal Issue: 4; Journal ID: ISSN 2169-8287

Publisher:: American Society for Microbiology

Country of Publication:: United States

Language:: English

Subject:: 59 BASIC BIOLOGICAL SCIENCES

Citation Formats


                    Everroad, R. C., Woebken, D., Singer, S. W., Burow, L. C., Kyrpides, N., Woyke, T., Goodwin, L., Detweiler, A., Prufert-Bebout, L., and Pett-Ridge, J. Draft Genome Sequence of an Oscillatorian Cyanobacterium, Strain ESFC-1.  United States: N. p., 2013. 
Web.  doi:10.1128/genomeA.00527-13.

Copy to clipboard


                    Everroad, R. C., Woebken, D., Singer, S. W., Burow, L. C., Kyrpides, N., Woyke, T., Goodwin, L., Detweiler, A., Prufert-Bebout, L., & Pett-Ridge, J. Draft Genome Sequence of an Oscillatorian Cyanobacterium, Strain ESFC-1.  United States.  https://doi.org/10.1128/genomeA.00527-13

Copy to clipboard


                    Everroad, R. C., Woebken, D., Singer, S. W., Burow, L. C., Kyrpides, N., Woyke, T., Goodwin, L., Detweiler, A., Prufert-Bebout, L., and Pett-Ridge, J. Thu .  
"Draft Genome Sequence of an Oscillatorian Cyanobacterium, Strain ESFC-1".  United States.  https://doi.org/10.1128/genomeA.00527-13.  https://www.osti.gov/servlets/purl/1524730.

Copy to clipboard


                    
@article{osti_1524730,

  title        = {Draft Genome Sequence of an Oscillatorian Cyanobacterium, Strain ESFC-1},

  author       = {Everroad, R. C. and Woebken, D. and Singer, S. W. and Burow, L. C. and Kyrpides, N. and Woyke, T. and Goodwin, L. and Detweiler, A. and Prufert-Bebout, L. and Pett-Ridge, J.},

  abstractNote = {The nonheterocystous filamentous cyanobacterium strain ESFC-1 has recently been isolated from a marine microbial mat system, where it was identified as belonging to a recently discovered lineage of active nitrogen-fixing microorganisms. Here, we report the draft genome sequence of this isolate. The assembly consists of 3 scaffolds and contains 5,632,035 bp with a GC content of 46.5%.},

  doi          = {10.1128/genomeA.00527-13},

  journal      = {Genome Announcements},

  number       = 4,

  volume       = 1,

  place        = {United States},

  year         = {Thu Aug 01 00:00:00 EDT 2013},

  month        = {Thu Aug 01 00:00:00 EDT 2013}

}

Copy to clipboard

Journal Article:

Free Publicly Available Full Text

Accepted Manuscript (DOE)

Publisher's Version of Record

https://doi.org/10.1128/genomeA.00527-13

Other availability

Search WorldCat to find libraries that may hold this journal

Save / Share:

Export Metadata

Save to My Library

Works referenced in this record:

Physiological ecology of cyanobacteria in microbial mats and other communities
journal, September 1995

Stal, Lucas J.
New Phytologist, Vol. 131, Issue 1
DOI: 10.1111/j.1469-8137.1995.tb03051.x

Identification of a novel cyanobacterial group as active diazotrophs in a coastal microbial mat using NanoSIMS analysis
journal, January 2012

Woebken, Dagmar; Burow, Luke C.; Prufert-Bebout, Leslie
The ISME Journal, Vol. 6, Issue 7
DOI: 10.1038/ismej.2011.200

Solexa Ltd
journal, June 2004

Bennett, Simon
Pharmacogenomics, Vol. 5, Issue 4
DOI: 10.1517/14622416.5.4.433

ALLPATHS: De novo assembly of whole-genome shotgun microreads
journal, February 2008

Butler, J.; MacCallum, I.; Kleber, M.
Genome Research, Vol. 18, Issue 5
DOI: 10.1101/gr.7337908

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

Zerbino, D. R.; Birney, E.
Genome Research, Vol. 18, Issue 5
DOI: 10.1101/gr.074492.107

Base-Calling of Automated Sequencer Traces Using Phred. II. Error Probabilities
journal, March 1998

Ewing, Brent; Green, Phil
Genome Research, Vol. 8, Issue 3
DOI: 10.1101/gr.8.3.186

Base-Calling of Automated Sequencer Traces Using Phred. I. Accuracy Assessment
journal, March 1998

Ewing, Brent; Hillier, LaDeana; Wendl, Michael C.
Genome Research, Vol. 8, Issue 3
DOI: 10.1101/gr.8.3.175

Consed: A Graphical Tool for Sequence Finishing
journal, March 1998

Gordon, David; Abajian, Chris; Green, Phil
Genome Research, Vol. 8, Issue 3
DOI: 10.1101/gr.8.3.195

The RAST Server: Rapid Annotations using Subsystems Technology
journal, January 2008

Aziz, Ramy K.; Bartels, Daniela; Best, Aaron A.
BMC Genomics, Vol. 9, Issue 1, Article No. 75
DOI: 10.1186/1471-2164-9-75

The integrated microbial genomes (IMG) system
journal, January 2006

Markowitz, V. M.
Nucleic Acids Research, Vol. 34, Issue 90001
DOI: 10.1093/nar/gkj024

Molecular and morphological characterization of cyanobacterial diversity in the stromatolites of Highborne Cay, Bahamas
journal, January 2009

Foster, Jamie S.; Green, Stefan J.; Ahrendt, Steven R.
The ISME Journal, Vol. 3, Issue 5
DOI: 10.1038/ismej.2008.129

Similar Records in DOE PAGES and OSTI.GOV collections:

Permanent draft genome of strain ESFC-1: ecological genomics of a newly discovered lineage of filamentous diazotrophic cyanobacteria

Journal Article Everroad, R. Craig ; Stuart, Rhona K. ; Bebout, Brad M. ; ... - Standards in Genomic Sciences

The nonheterocystous filamentous cyanobacterium, strain ESFC-1, is a recently described member of the order Oscillatoriales within the Cyanobacteria. ESFC-1 has been shown to be a major diazotroph in the intertidal microbial mat system at Elkhorn Slough, CA, USA. Based on phylogenetic analyses of the 16S RNA gene, ESFC-1 appears to belong to a unique, genus-level divergence; the draft genome sequence of this strain has now been determined. Here we report features of this genome as they relate to the ecological functions and capabilities of strain ESFC-1. The 5,632,035 bp genome sequence encodes 4914 protein-coding genes and 92 RNA genes. Onemore »« less
Cited by 4
https://doi.org/10.1186/s40793-016-0174-6

Full Text Available
Draft genome sequence of marine alphaproteobacterial strain HIMB11, the first cultivated representative of a unique lineage within the Roseobacter clade possessing an unusually small genome

Journal Article Durham, Bryndan P. ; Grote, Jana ; Whittaker, Kerry A. ; ... - Standards in Genomic Sciences

Strain HIMB11 is a planktonic marine bacterium isolated from coastal seawater in Kaneohe Bay, Oahu, Hawaii belonging to the ubiquitous and versatile Roseobacter clade of the alphaproteobacterial family Rhodobacteraceae. Here we describe the preliminary characteristics of strain HIMB11, including annotation of the draft genome sequence and comparative genomic analysis with other members of the Roseobacter lineage. The 3,098,747 bp draft genome is arranged in 34 contigs and contains 3,183 protein-coding genes and 54 RNA genes. Phylogenomic and 16S rRNA gene analyses indicate that HIMB11 represents a unique sublineage within the Roseobacter clade. Comparison with other publicly available genome sequences frommore »« less
https://doi.org/10.4056/sigs.4998989

Full Text Available
A Systems Biology Approach to Energy Flow in H₂ Producing Microbial Communities: Microbial Mats

Technical Report Bebout, Brad M. ; Bebout, Leslie E. ; Everroad, R. Craig ; ...

This report describes the results of work conducted at NASA Ames Research Center, in collaboration with investigators at Lawrence Livermore National Laboratory, during the time period 12/15/2014 to 12/15/2017. The work was an extension of a collaboration with LLNL that began in 2008. Work this reporting period focused primarily on tasks related to microbial mats from both the Elkhorn Slough and Baja California field sites, including the analysis and publication of data produced prior to 12/15/2014. During this reporting period, in addition to the microbial mat work, we also conducted a series of experiments with a particular algal-bacterial association (C.more »« less
https://doi.org/10.2172/1425657

Full Text Available
High-quality permanent draft genome sequence of the Mimosa asperata - nodulating Cupriavidus sp. strain AMP6

Journal Article De Meyer, Sofie E. ; Parker, Matthew ; Van Berkum, Peter ; ... - Standards in Genomic Sciences

Â© 2015 De Meyer et al. Cupriavidus sp. strain AMP6 is an aerobic, motile, Gram-negative, non-spore-forming rod that was isolated from a root nodule of Mimosa asperata collected in Santa Ana National Wildlife Refuge, Texas, in 2005. Mimosa asperata is the only legume described so far to exclusively associates with Cupriavidus symbionts. Moreover, strain AMP6 represents an early-diverging lineage within the symbiotic Cupriavidus group and has the capacity to develop an effective nitrogen-fixing symbiosis with three other species of Mimosa. Therefore, the genome of Cupriavidus sp. strain AMP6 enables comparative analyses of symbiotic trait evolution in this genus and heremore »« less
https://doi.org/10.1186/s40793-015-0074-1

Full Text Available
High-quality permanent draft genome sequence of the Bradyrhizobium elkanii type strain USDA 76T, isolated from Glycine max (L.) Merr

Journal Article Reeve, Wayne ; van Berkum, Peter ; Ardley, Julie ; ... - Standards in Genomic Sciences

Bradyrhizobium elkanii USDA 76 ^T (INSCD = ARAG00000000), the type strain for Bradyrhizobium elkanii, is an aerobic, motile, Gram-negative, non-spore-forming rod that was isolated from an effective nitrogen-fixing root nodule of Glycine max (L. Merr) grown in the USA. Because of its significance as a microsymbiont of this economically important legume, B. elkanii USDA 76 ^T was selected as part of the DOE Joint Genome Institute 2010 Genomic Encyclopedia for Bacteria and Archaea-Root Nodule Bacteria sequencing project. Here the symbiotic abilities of B. elkanii USDA 76 ^T are described, together with its genome sequence information and annotation. The 9,484,767 bpmore »« less
Cited by 7
https://doi.org/10.1186/s40793-017-0238-2

Full Text Available

Similar Records

Title: Draft Genome Sequence of an Oscillatorian Cyanobacterium, Strain ESFC-1

Abstract

Citation Formats

Physiological ecology of cyanobacteria in microbial mats and other communities journal, September 1995

Identification of a novel cyanobacterial group as active diazotrophs in a coastal microbial mat using NanoSIMS analysis journal, January 2012

Solexa Ltd journal, June 2004

ALLPATHS: De novo assembly of whole-genome shotgun microreads journal, February 2008

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

Base-Calling of Automated Sequencer Traces Using Phred. II. Error Probabilities journal, March 1998

Base-Calling of Automated Sequencer Traces Using Phred. I. Accuracy Assessment journal, March 1998

Consed: A Graphical Tool for Sequence Finishing journal, March 1998

The RAST Server: Rapid Annotations using Subsystems Technology journal, January 2008

The integrated microbial genomes (IMG) system journal, January 2006

Molecular and morphological characterization of cyanobacterial diversity in the stromatolites of Highborne Cay, Bahamas journal, January 2009

Physiological ecology of cyanobacteria in microbial mats and other communities
journal, September 1995

Identification of a novel cyanobacterial group as active diazotrophs in a coastal microbial mat using NanoSIMS analysis
journal, January 2012

Solexa Ltd
journal, June 2004

ALLPATHS: De novo assembly of whole-genome shotgun microreads
journal, February 2008

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

Base-Calling of Automated Sequencer Traces Using Phred. II. Error Probabilities
journal, March 1998

Base-Calling of Automated Sequencer Traces Using Phred. I. Accuracy Assessment
journal, March 1998

Consed: A Graphical Tool for Sequence Finishing
journal, March 1998

The RAST Server: Rapid Annotations using Subsystems Technology
journal, January 2008

The integrated microbial genomes (IMG) system
journal, January 2006

Molecular and morphological characterization of cyanobacterial diversity in the stromatolites of Highborne Cay, Bahamas
journal, January 2009