skip to main content
DOE PAGES title logo U.S. Department of Energy
Office of Scientific and Technical Information

Title: Genome sequence of Shimia str. SK013, a representative of the Roseobacter group isolated from marine sediment

Authors:
; ; ; ; ; ; ; ; ; ; ;
Publication Date:
Research Org.:
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) (SC-23)
OSTI Identifier:
1618955
Alternate Identifier(s):
OSTI ID: 1288270; OSTI ID: 1379156
Grant/Contract Number:  
AC02-05CH11231
Resource Type:
Published Article
Journal Name:
Standards in Genomic Sciences
Additional Journal Information:
Journal Name: Standards in Genomic Sciences Journal Volume: 11 Journal Issue: 1; Journal ID: ISSN 1944-3277
Publisher:
Springer Science + Business Media
Country of Publication:
United Kingdom
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; anaerobic metabolism; cell-connecting filaments; quorum quenching; flagella gene cluster; DMSP; DMSO reductase; denitrification; homoserine lactone acylase; escherichia-coli k-12; sp-nov.; emended description; rna genes; bacteria; system; clade; identification; annotation

Citation Formats

Kanukollu, Saranya, Voget, Sonja, Pohlner, Marion, Vandieken, Verona, Petersen, Jörn, Kyrpides, Nikos C., Woyke, Tanja, Shapiro, Nicole, Göker, Markus, Klenk, Hans-Peter, Cypionka, Heribert, and Engelen, Bert. Genome sequence of Shimia str. SK013, a representative of the Roseobacter group isolated from marine sediment. United Kingdom: N. p., 2016. Web. doi:10.1186/s40793-016-0143-0.
Kanukollu, Saranya, Voget, Sonja, Pohlner, Marion, Vandieken, Verona, Petersen, Jörn, Kyrpides, Nikos C., Woyke, Tanja, Shapiro, Nicole, Göker, Markus, Klenk, Hans-Peter, Cypionka, Heribert, & Engelen, Bert. Genome sequence of Shimia str. SK013, a representative of the Roseobacter group isolated from marine sediment. United Kingdom. doi:10.1186/s40793-016-0143-0.
Kanukollu, Saranya, Voget, Sonja, Pohlner, Marion, Vandieken, Verona, Petersen, Jörn, Kyrpides, Nikos C., Woyke, Tanja, Shapiro, Nicole, Göker, Markus, Klenk, Hans-Peter, Cypionka, Heribert, and Engelen, Bert. Sat . "Genome sequence of Shimia str. SK013, a representative of the Roseobacter group isolated from marine sediment". United Kingdom. doi:10.1186/s40793-016-0143-0.
@article{osti_1618955,
title = {Genome sequence of Shimia str. SK013, a representative of the Roseobacter group isolated from marine sediment},
author = {Kanukollu, Saranya and Voget, Sonja and Pohlner, Marion and Vandieken, Verona and Petersen, Jörn and Kyrpides, Nikos C. and Woyke, Tanja and Shapiro, Nicole and Göker, Markus and Klenk, Hans-Peter and Cypionka, Heribert and Engelen, Bert},
abstractNote = {},
doi = {10.1186/s40793-016-0143-0},
journal = {Standards in Genomic Sciences},
number = 1,
volume = 11,
place = {United Kingdom},
year = {2016},
month = {3}
}

Journal Article:
Free Publicly Available Full Text
Publisher's Version of Record
DOI: 10.1186/s40793-016-0143-0

Citation Metrics:
Cited by: 1 work
Citation information provided by
Web of Science

Save / Share:

Works referenced in this record:

Improved Prediction of Signal Peptides: SignalP 3.0
journal, July 2004

  • Dyrløv Bendtsen, Jannick; Nielsen, Henrik; von Heijne, Gunnar
  • Journal of Molecular Biology, Vol. 340, Issue 4, p. 783-795
  • DOI: 10.1016/j.jmb.2004.05.028

Rfam 12.0: updates to the RNA families database
journal, November 2014

  • Nawrocki, Eric P.; Burge, Sarah W.; Bateman, Alex
  • Nucleic Acids Research, Vol. 43, Issue D1
  • DOI: 10.1093/nar/gku1063

Type IV pilus structure and bacterial pathogenicity
journal, May 2004

  • Craig, Lisa; Pique, Michael E.; Tainer, John A.
  • Nature Reviews Microbiology, Vol. 2, Issue 5
  • DOI: 10.1038/nrmicro885

ARB: a software environment for sequence data
journal, February 2004


QUORUM SENSING: Cell-to-Cell Communication in Bacteria
journal, November 2005


Shimia sagamensis sp. nov., a marine bacterium isolated from cold-seep sediment
journal, September 2015

  • Uchida, Hiromi; Hatada, Yuji; Mori, Kozue
  • International Journal of Systematic and Evolutionary Microbiology, Vol. 65, Issue 9
  • DOI: 10.1099/ijs.0.000333

SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing
journal, May 2012

  • Bankevich, Anton; Nurk, Sergey; Antipov, Dmitry
  • Journal of Computational Biology, Vol. 19, Issue 5
  • DOI: 10.1089/cmb.2012.0021

Identification of Extracellular N-Acylhomoserine Lactone Acylase from a Streptomyces sp. and Its Application to Quorum Quenching
journal, May 2005


RNAmmer: consistent and rapid annotation of ribosomal RNA genes
journal, April 2007

  • Lagesen, Karin; Hallin, Peter; Rødland, Einar Andreas
  • Nucleic Acids Research, Vol. 35, Issue 9
  • DOI: 10.1093/nar/gkm160

Structure of the Bundle-forming Pilus from Enteropathogenic Escherichia coli
journal, September 2005

  • Ramboarina, Stéphanie; Fernandes, Paula J.; Daniell, Sarah
  • Journal of Biological Chemistry, Vol. 280, Issue 48
  • DOI: 10.1074/jbc.M508099200

Shimia biformata sp. nov., isolated from surface seawater, and emended description of the genus Shimia Choi and Cho 2006
journal, August 2013

  • Hameed, A.; Shahina, M.; Lin, S. -Y.
  • INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Vol. 63, Issue Pt 12
  • DOI: 10.1099/ijs.0.053553-0

Shimia isoporae sp. nov., isolated from the reef-building coral Isopora palifera
journal, May 2010

  • Chen, M. -H.; Sheu, S. -Y.; Chen, C. A.
  • INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Vol. 61, Issue 4
  • DOI: 10.1099/ijs.0.022848-0

Diversity, ecology, and genomics of the Roseobacter clade: a short overview
journal, February 2008

  • Brinkhoff, Thorsten; Giebel, Helge-Ansgar; Simon, Meinhard
  • Archives of Microbiology, Vol. 189, Issue 6
  • DOI: 10.1007/s00203-008-0353-y

Essential roles for the products of the napABCD genes, but not napFGH, in periplasmic nitrate reduction by Escherichia coli K-12
journal, November 1999

  • Potter, Laura C.; Cole, Jeffrey A.
  • Biochemical Journal, Vol. 344, Issue 1
  • DOI: 10.1042/bj3440069

Trimmomatic: a flexible trimmer for Illumina sequence data
journal, April 2014


Predicting transmembrane protein topology with a hidden markov model: application to complete genomes11Edited by F. Cohen
journal, January 2001

  • Krogh, Anders; Larsson, Björn; von Heijne, Gunnar
  • Journal of Molecular Biology, Vol. 305, Issue 3
  • DOI: 10.1006/jmbi.2000.4315

Distinct compositions of free-living, particle-associated and benthic communities of the Roseobacter group in the North Sea
journal, November 2015

  • Kanukollu, Saranya; Wemheuer, Bernd; Herber, Janina
  • FEMS Microbiology Ecology, Vol. 92, Issue 1
  • DOI: 10.1093/femsec/fiv145

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

Roseobacter clade bacteria are abundant in coastal sediments and encode a novel combination of sulfur oxidation genes
journal, June 2012

  • Lenk, Sabine; Moraru, Cristina; Hahnke, Sarah
  • The ISME Journal, Vol. 6, Issue 12
  • DOI: 10.1038/ismej.2012.66

Periplasmic Nitrate Reductase (NapABC Enzyme) Supports Anaerobic Respiration by Escherichia coli K-12
journal, March 2002


Ocean's Twelve: flagellar and biofilm chromids in the multipartite genome of M arinovum algicola  DG898 exemplify functional compartmentalization : The genome of
journal, September 2015

  • Frank, Oliver; Göker, Markus; Pradella, Silke
  • Environmental Microbiology, Vol. 17, Issue 10
  • DOI: 10.1111/1462-2920.12947

BLAST Ring Image Generator (BRIG): simple prokaryote genome comparisons
journal, August 2011

  • Alikhan, Nabil-Fareed; Petty, Nicola K.; Ben Zakour, Nouri L.
  • BMC Genomics, Vol. 12, Issue 1
  • DOI: 10.1186/1471-2164-12-402

Bacterial quorum sensing and metabolic slowing in a cooperative population
journal, September 2014

  • An, J. H.; Goo, E.; Kim, H.
  • Proceedings of the National Academy of Sciences, Vol. 111, Issue 41
  • DOI: 10.1073/pnas.1412431111

The Genomes On Line Database (GOLD) in 2009: status of genomic and metagenomic projects and their associated metadata
journal, November 2009

  • Liolios, Konstantinos; Chen, I-Min A.; Mavromatis, Konstantinos
  • Nucleic Acids Research, Vol. 38, Issue suppl_1
  • DOI: 10.1093/nar/gkp848

Shimia marina gen. nov., sp. nov., a novel bacterium of the Roseobacter clade isolated from biofilm in a coastal fish farm
journal, August 2006

  • Choi, D. H.
  • INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Vol. 56, Issue 8
  • DOI: 10.1099/ijs.0.64235-0

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

tRNAscan-SE: A Program for Improved Detection of Transfer RNA Genes in Genomic Sequence
journal, March 1997


Genomic Encyclopedia of Type Strains, Phase I: The one thousand microbial genomes (KMG-I) project
journal, December 2013

  • Kyrpides, Nikos C.; Woyke, Tanja; Eisen, Jonathan A.
  • Standards in Genomic Sciences, Vol. 9, Issue 3
  • DOI: 10.4056/sigs.5068949

Genome sequence-based species delimitation with confidence intervals and improved distance functions
journal, January 2013

  • Meier-Kolthoff, Jan P.; Auch, Alexander F.; Klenk, Hans-Peter
  • BMC Bioinformatics, Vol. 14, Issue 1
  • DOI: 10.1186/1471-2105-14-60

Identification of QuiP, the Product of Gene PA1032, as the Second Acyl-Homoserine Lactone Acylase of Pseudomonas aeruginosa PAO1
journal, February 2006


Genomic Encyclopedia of Bacteria and Archaea: Sequencing a Myriad of Type Strains
journal, August 2014


IMG 4 version of the integrated microbial genomes comparative analysis system
journal, October 2013

  • Markowitz, Victor M.; Chen, I-Min A.; Palaniappan, Krishna
  • Nucleic Acids Research, Vol. 42, Issue D1
  • DOI: 10.1093/nar/gkt963

antiSMASH 3.0—a comprehensive resource for the genome mining of biosynthetic gene clusters
journal, May 2015

  • Weber, Tilmann; Blin, Kai; Duddela, Srikanth
  • Nucleic Acids Research, Vol. 43, Issue W1
  • DOI: 10.1093/nar/gkv437

Environmental Biology of the Marine Roseobacter Lineage
journal, October 2006


Digital DNA-DNA hybridization for microbial species delineation by means of genome-to-genome sequence comparison
journal, January 2010

  • Auch, Alexander F.; von Jan, Mathias; Klenk, Hans-Peter
  • Standards in Genomic Sciences, Vol. 2, Issue 1
  • DOI: 10.4056/sigs.531120

Shimia haliotis sp. nov., a bacterium isolated from the gut of an abalone, Haliotis discus hannai
journal, June 2013

  • Hyun, D. -W.; Kim, M. -S.; Shin, N. -R.
  • INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Vol. 63, Issue Pt 11
  • DOI: 10.1099/ijs.0.053140-0

Transformation of Sulfur Compounds by an Abundant Lineage of Marine Bacteria in the α-Subclass of the ClassProteobacteria
journal, September 1999


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


Evolutionary Ecology of the Marine Roseobacter Clade
journal, November 2014

  • Luo, Haiwei; Moran, Mary Ann
  • Microbiology and Molecular Biology Reviews, Vol. 78, Issue 4
  • DOI: 10.1128/MMBR.00020-14

Linking a Bacterial Taxon to Sulfur Cycling in the Sea: Studies of the Marine Roseobacter Group
journal, July 2003

  • Moran, Mary Ann; González, José M.; Kiene, Ronald P.
  • Geomicrobiology Journal, Vol. 20, Issue 4
  • DOI: 10.1080/01490450303901

Genome sequence and emended description of Leisingera nanhaiensis strain DSM 24252T isolated from marine sediment
journal, January 2014

  • Breider, Sven; Teshima, Hazuki; Petersen, Jörn
  • Standards in Genomic Sciences, Vol. 9, Issue 3
  • DOI: 10.4056/sigs.3828824

A Complete Set of Flagellar Genes Acquired by Horizontal Transfer Coexists with the Endogenous Flagellar System in Rhodobacter sphaeroides
journal, February 2007

  • Poggio, S.; Abreu-Goodger, C.; Fabela, S.
  • Journal of Bacteriology, Vol. 189, Issue 8
  • DOI: 10.1128/JB.01681-06

Genome characteristics of a generalist marine bacterial lineage
journal, January 2010

  • Newton, Ryan J.; Griffin, Laura E.; Bowles, Kathy M.
  • The ISME Journal, Vol. 4, Issue 6
  • DOI: 10.1038/ismej.2009.150

Quantitative analysis of bacterial communities from Mediterranean sapropels based on cultivation-dependent methods
journal, December 2004